Step 4 (final) of the three-step ctwasPipeline:
runs ctwas::finemap_regions on the screened-region set from
screenCtwasRegions and assembles the documented top-level
ctwas output (z_gene, param, finemap_res,
susie_alpha_res, region_data, boundary_genes,
screen_res).
Usage
finemapCtwasRegions(
screenResult,
maxNumSingleEffects = 5L,
numThreads = 1L,
methodArgs = CtwasOptions()
)Arguments
- screenResult
A list returned by
screenCtwasRegions.- maxNumSingleEffects
Pass-through.
- numThreads
Number of cores.
- methodArgs
Additional arguments forwarded to ctwas, built with
CtwasOptions. Names are checked against what the ctwas steps accept between them.
Value
A list mirroring ctwas::ctwas_sumstats's output:
z_gene, param, finemap_res, susie_alpha_res,
region_data, boundary_genes, screen_res.
Examples
data(ctwasWeightsExample)
ldDir <- system.file("extdata", "ld_reference", "chr22",
package = "pecotmr")
ldStem <- file.path(ldDir, "protocol_example.LD.chr22")
gwasTsv <- system.file("extdata", "manifests",
"protocol_example.twas.gwas_sumstats.chr22.tsv.gz", package = "pecotmr")
mani <- data.frame(study = "gwas1", sumStatsPath = gwasTsv)
blocks <- GenomicRanges::GRanges("chr22",
IRanges::IRanges(c(10000000, 15000001), c(15000000, 19000000)),
blockId = c("chr22_1", "chr22_2"))
gss <- loadGwasSumStatsFromManifest(manifest = mani, genome = "hg38",
ldReference = ldStem, region = "chr22:10000000-19000000",
ldBlocks = blocks)
#> Warning: GwasSumStats[study=gwas1]: no effect-allele frequency declared (map `af: <col>` to export a directional af); top_loci$af will be NA. A directionless `maf`/`FRQ` is used for QC only, never as af.
gwasByRegion <- summaryStatsQc(gss,
panelFilterParam = PanelFilterParam(mafCutoff = 0.0025))
#> [gwas1] QC track: harmonization kept 20 of 20 variant(s) (corrected: sign-flipped 0, strand-flipped 0; dropped 0).
#> [gwas1] QC summary: 20 in -> 20 out | corrected: sign-flip 0, strand-flip 0
#> [gwas1] QC track: harmonization kept 155 of 155 variant(s) (corrected: sign-flipped 0, strand-flipped 0; dropped 0).
#> [gwas1] QC summary: 155 in -> 155 out | corrected: sign-flip 0, strand-flip 0
inp <- assembleCtwasInputs(gwasSumStats = gwasByRegion,
twasWeights = list(ctwasWeightsExample))
est <- estCtwasGroupPriors(inp,
ctwasPriorParam = CtwasPriorParam(thin = 1, niterPrefit = 3, niter = 10,
fallbackToPrefit = TRUE),
methodArgs = CtwasOptions(
regionData = CtwasRegionDataOptions(min_group_size = 1),
estParam = CtwasEstParamOptions(
min_group_size = 1, min_p_single_effect = 0
)
))
screened <- screenCtwasRegions(est)
finemapCtwasRegions(screened, maxNumSingleEffects = 5L)
#> $z_gene
#> id z
#> 1 chr22_1|protocol_example|bulk_rnaseq|ENSG00000130538|susie 1.826089
#> type context group
#> 1 bulk_rnaseq bulk_rnaseq bulk_rnaseq|bulk_rnaseq
#>
#> $param
#> $param$group_size
#> bulk_rnaseq|bulk_rnaseq SNP
#> 1 173
#>
#> $param$group_prior
#> bulk_rnaseq|bulk_rnaseq SNP
#> 0.01326949 0.02400648
#>
#> $param$group_prior_var
#> bulk_rnaseq|bulk_rnaseq SNP
#> 2.368016 4.549256
#>
#> $param$group_prior_iters
#> iter1 iter2 iter3
#> bulk_rnaseq|bulk_rnaseq 0.01480974 0.01401405 0.01326949
#> SNP 0.02402130 0.02399932 0.02400648
#>
#> $param$group_prior_var_iters
#> iter1 iter2 iter3
#> bulk_rnaseq|bulk_rnaseq 2.469631 2.401220 2.368016
#> SNP 4.652935 4.580147 4.549256
#>
#> $param$loglik_iters
#> iter1 iter2 iter3
#> 0.1576888 0.1579842 0.1580717
#>
#> $param$group_prior_var_structure
#> [1] "shared_type"
#>
#> $param$converged
#> [1] TRUE
#>
#>
#> $finemap_res
#> NULL
#>
#> $susie_alpha_res
#> NULL
#>
#> $region_data
#> $region_data$chr22_1
#> $region_data$chr22_1$region_id
#> [1] "chr22_1"
#>
#> $region_data$chr22_1$chrom
#> [1] 22
#>
#> $region_data$chr22_1$start
#> [1] 10685239
#>
#> $region_data$chr22_1$stop
#> [1] 12640661
#>
#> $region_data$chr22_1$minpos
#> [1] 10685239
#>
#> $region_data$chr22_1$maxpos
#> [1] 18850784
#>
#> $region_data$chr22_1$thin
#> [1] 1
#>
#> $region_data$chr22_1$gid
#> [1] "chr22_1|protocol_example|bulk_rnaseq|ENSG00000130538|susie"
#>
#> $region_data$chr22_1$sid
#> [1] "chr22:10685239:C:T"
#> [2] "chr22:10761227:G:A"
#> [3] "chr22:11285239:C:T"
#> [4] "chr22:11601805:G:A"
#> [5] "chr22:11791698:G:T"
#> [6] "chr22:11797697:C:T"
#> [7] "chr22:12044872:A:C"
#> [8] "chr22:12194389:G:A"
#> [9] "chr22:12207043:C:T"
#> [10] "chr22:12350816:G:A"
#> [11] "chr22:12352464:C:A"
#> [12] "chr22:12370627:C:T"
#> [13] "chr22:12383838:G:A"
#> [14] "chr22:12571373:AGAAAGAAAGAAAGAAAGAAG:*"
#> [15] "chr22:12571377:AGAAAGAAAGAAAGAAG:*"
#> [16] "chr22:12571385:AGAAAGAAG:*"
#> [17] "chr22:12571386:GAAAGAAGGA:*"
#> [18] "chr22:12571389:AGAAGGAAAGAAGGAAAGAAAGGAAGAAGGAAAGAAG:*"
#> [19] "chr22:12576050:T:A"
#>
#> $region_data$chr22_1$z_gene
#> id z
#> 1 chr22_1|protocol_example|bulk_rnaseq|ENSG00000130538|susie 1.826089
#> type context group
#> 1 bulk_rnaseq bulk_rnaseq bulk_rnaseq|bulk_rnaseq
#>
#> $region_data$chr22_1$z_snp
#> id z type
#> 1 chr22:10685239:C:T 0.6698973 SNP
#> 2 chr22:10761227:G:A -2.9338401 SNP
#> 3 chr22:11285239:C:T -1.4610873 SNP
#> 4 chr22:11601805:G:A 1.3802499 SNP
#> 5 chr22:11791698:G:T 0.9190242 SNP
#> 6 chr22:11797697:C:T -1.1206492 SNP
#> 7 chr22:12044872:A:C 1.5922033 SNP
#> 8 chr22:12194389:G:A 0.3413515 SNP
#> 9 chr22:12207043:C:T -0.1974221 SNP
#> 10 chr22:12350816:G:A -2.4507725 SNP
#> 11 chr22:12352464:C:A 0.7036564 SNP
#> 12 chr22:12370627:C:T 1.4911500 SNP
#> 13 chr22:12383838:G:A -0.7999027 SNP
#> 14 chr22:12571373:AGAAAGAAAGAAAGAAAGAAG:* 0.7017074 SNP
#> 15 chr22:12571377:AGAAAGAAAGAAAGAAG:* -1.1544826 SNP
#> 16 chr22:12571385:AGAAAGAAG:* -0.8857574 SNP
#> 17 chr22:12571386:GAAAGAAGGA:* -2.3568861 SNP
#> 18 chr22:12571389:AGAAGGAAAGAAGGAAAGAAAGGAAGAAGGAAAGAAG:* 1.5041306 SNP
#> 19 chr22:12576050:T:A -0.6426061 SNP
#> context group
#> 1 SNP SNP
#> 2 SNP SNP
#> 3 SNP SNP
#> 4 SNP SNP
#> 5 SNP SNP
#> 6 SNP SNP
#> 7 SNP SNP
#> 8 SNP SNP
#> 9 SNP SNP
#> 10 SNP SNP
#> 11 SNP SNP
#> 12 SNP SNP
#> 13 SNP SNP
#> 14 SNP SNP
#> 15 SNP SNP
#> 16 SNP SNP
#> 17 SNP SNP
#> 18 SNP SNP
#> 19 SNP SNP
#>
#> $region_data$chr22_1$types
#> [1] "bulk_rnaseq" "SNP"
#>
#> $region_data$chr22_1$contexts
#> [1] "bulk_rnaseq" "SNP"
#>
#> $region_data$chr22_1$groups
#> [1] "bulk_rnaseq|bulk_rnaseq" "SNP"
#>
#>
#> $region_data$chr22_2
#> $region_data$chr22_2$region_id
#> [1] "chr22_2"
#>
#> $region_data$chr22_2$chrom
#> [1] 22
#>
#> $region_data$chr22_2$start
#> [1] 15574750
#>
#> $region_data$chr22_2$stop
#> [1] 18850784
#>
#> $region_data$chr22_2$minpos
#> [1] 15574750
#>
#> $region_data$chr22_2$maxpos
#> [1] 18731027
#>
#> $region_data$chr22_2$thin
#> [1] 1
#>
#> $region_data$chr22_2$gid
#> character(0)
#>
#> $region_data$chr22_2$sid
#> [1] "chr22:15574750:C:A"
#> [2] "chr22:15635104:C:A"
#> [3] "chr22:15689224:A:C"
#> [4] "chr22:15773180:G:A"
#> [5] "chr22:15837995:CTTTCTTTCTTTCTTTTTCTTT:CTTTTTCTTTCTTTCTTTTTCTTT"
#> [6] "chr22:15838001:TTCTTTCTTTTTCTTTC:TTTTCTTTTTCTTTC"
#> [7] "chr22:15838002:TCTTTCTTTTTCTTTCTTC:*"
#> [8] "chr22:15838003:CTTTCTTTTTCTTT:ATTTCTTTTTCTTT"
#> [9] "chr22:15838003:CTTTCTTTTTCTTT:CTTTTTCTTTTTCTTT"
#> [10] "chr22:15838010:TTTCTTTCTTCCTTCCTTCCTTCCTTCCTTCCTCCCTTCCTTC:TCTTCTTTCTTCCTTCCTTCCTTCCTTCCTTCCTCCCTTCCTTC"
#> [11] "chr22:15839920:G:A"
#> [12] "chr22:15919156:A:T"
#> [13] "chr22:15927084:C:T"
#> [14] "chr22:15947643:T:C"
#> [15] "chr22:15984722:T:C"
#> [16] "chr22:16073625:G:T"
#> [17] "chr22:16102937:C:T"
#> [18] "chr22:16111042:C:CA"
#> [19] "chr22:16112049:C:A"
#> [20] "chr22:16112091:TG:CG"
#> [21] "chr22:16115854:C:T"
#> [22] "chr22:16124912:C:T"
#> [23] "chr22:16132992:A:G"
#> [24] "chr22:16187126:A:G"
#> [25] "chr22:16207293:A:G"
#> [26] "chr22:16214693:C:A"
#> [27] "chr22:16217062:A:G"
#> [28] "chr22:16224528:T:C"
#> [29] "chr22:16234309:C:T"
#> [30] "chr22:16244919:T:C"
#> [31] "chr22:16254612:GGAAGGAAGGAAGGAAA:AGAAGGAAGGAAGGAAA"
#> [32] "chr22:16258960:C:A"
#> [33] "chr22:16262035:G:A"
#> [34] "chr22:16262334:GATTCCATTCGATGATTCCATTCA:G"
#> [35] "chr22:16262336:TTCCATTCGATGATTCCATTCAATTCCATTCGATGATGATTCCATTCGAG:*"
#> [36] "chr22:16262338:CCATTCGATGATTCCATTCAA:*"
#> [37] "chr22:16386749:TCCGCCGCCGCCGCGGCTTTTTGCCCCCCACCCCCGCCGCCGCGGCTTTTTACCCGCCGCGGCTTTTTGCCCCCCCGCCGCCGTGGTTTTTTCCCCCCATCTCACCTCCGCTTTTTGCCCGCCGCGGCTTTTTGCCCCCACCCCGCCTCGGCTTTTTGCCAGCCACGGCTTTTTGCCCCCCGCCACCGCGGCTTTTTGTCCC:*"
#> [38] "chr22:16386751:CGCCGCCGCCGCGGCTTTTTGCCCCCCACCCCCGCCGCCGCGGCTTTTTACCCGCCGCGGCTTTTTGCCCCCCCG:*"
#> [39] "chr22:16386752:GCCGCCGCCGCGGCTTTTTGCCCCCCACCCCCGCCGCCGCGGCTTTTTACCCGCCGCGGCTTTTTGCCCCCCCGCCGCCGTGGTTTTTTCCCCCCATCTCACCTCCGCTTTTTGCCCGCCGCGGCTTTTTGCCCCCACCCCGCCTCGGCTTTTTGCCAGCCACGGCTTTTTGCCCC:CCCGCCGCCGCGGCTTTTTGCCCCCCACCCCCGCCGCCGCGGCTTTTTACCCGCCGCGGCTTTTTGCCCCCCCGCCGCCGTGGTTTTTTCCCCCCATCTCACCTCCGCTTTTTGCCCGCCGCGGCTTTTTGCCCCCACCCCGCCTCGGCTTTTTGCCAGCCACGGCTTTTTGCCCC"
#> [40] "chr22:16400343:T:C"
#> [41] "chr22:16427771:T:C"
#> [42] "chr22:16439458:A:G"
#> [43] "chr22:16442170:G:A"
#> [44] "chr22:16549730:A:G"
#> [45] "chr22:16560460:ACAGCCAGCCAGCCAAGCCAGCCAAGCCAGCCAGGAAAGCCAGCCTGCCAAGCCAGCCAAGCCAGCCAGCCACTCAAGCCAGCCAAGTCAGCGAGCCAACCAAGCCAGCCAACTCAGCCAGCCACCTAAGCCAGCCAAGCCAGCCAGCCAGCCAAGCAAGCCAGCCAGCCAAGCCAGCCAAGCCAGCCAAGCCAGGCAGCCAGCCAAGCCAGCCAAGCCAGCCAGCCAGCCAAGCCAGCCAGCCAGCCCACACAGCCAAGC:*"
#> [46] "chr22:16560533:TCAAGCCAGCCAAGTCAGCGAGCCAACCAAGCCAGCCAACTCAGCCAGCCACCTAAGCCAGCCAAGCCAGCCAGCCAGCCAAGCAAGCCAGCCAGCCAAGCCAGCCAAGCCAGCCAAGCCAGGCAGCCAGC:CCAAGCCAGCCAAGTCAGCGAGCCAACCAAGCCAGCCAACTCAGCCAGCCACCTAAGCCAGCCAAGCCAGCCAGCCAGCCAAGCAAGCCAGCCAGCCAAGCCAGCCAAGCCAGCCAAGCCAGGCAGCCAGC"
#> [47] "chr22:16566547:ACAGCCAAGACAGCCAGCCAGCCACGCAAGCCAAGCCAGCCAGCCAGGCAAGCCAGGCATGCCAGCCAAGCCATCCAGCCAGCCAAGCCAGGCGGCCAGCCAAGCCAGCCAAGCCACCCGGCCAGCCAAGCCACCCAAGCCACCCGGCCAGCCAGGCATCCAAGCCAGCCAAGT:*"
#> [48] "chr22:16566742:CAAGCCAGCCAGCTAGCCAAGCCACCCAGCCAGCCAGCCAGCCAAACCAGCCAAGCCAGCCAGCCAGCCAGCCAAGCCAGCCAAGCAAGCCAGCCAGCCAGCCAAGCCACGCAAGCCAGCCAGCCAGCCATGCCAGCCA:TAAGCCAGCCAGCTAGCCAAGCCACCCAGCCAGCCAGCCAGCCAAACCAGCCAAGCCAGCCAGCCAGCCAGCCAAGCCAGCCAAGCAAGCCAGCCAGCCAGCCAAGCCACGCAAGCCAGCCAGCCAGCCATGCCAGCCA"
#> [49] "chr22:16841646:CAAAAAAAAAAAAAA:AAAAAAAAAAAAAAA"
#> [50] "chr22:16845585:TCA:TCACA"
#> [51] "chr22:16909478:TCTCTCC:*"
#> [52] "chr22:16909479:CTCTCCCTCTCTCTCTCTCTCTCTCCCT:CCCCTCTCTCTCTCTCTCTCTCCCT"
#> [53] "chr22:16909480:TCTCCCTCTCTCTCTCTCTCTCTCC:*"
#> [54] "chr22:16909481:CTCCCTCTCTCTCTCTCTCTCTCCCT:*"
#> [55] "chr22:16970638:G:A"
#> [56] "chr22:16973012:G:A"
#> [57] "chr22:17014255:C:T"
#> [58] "chr22:17051853:C:T"
#> [59] "chr22:17079499:GAAAAAAA:GAAAAAAAA"
#> [60] "chr22:17113082:AG:A"
#> [61] "chr22:17136539:C:T"
#> [62] "chr22:17154616:CTT:CTTT"
#> [63] "chr22:17154616:CTTT:CT"
#> [64] "chr22:17157085:TACACACAC:CACACACAC"
#> [65] "chr22:17157085:TACACACAC:T"
#> [66] "chr22:17157085:TACACACAC:TACACACACACACACAC"
#> [67] "chr22:17157085:TACACACAC:TACACACACACACACACACAC"
#> [68] "chr22:17157085:TACACACAC:TACACACACACACACACACACACAC"
#> [69] "chr22:17168884:C:T"
#> [70] "chr22:17172477:C:T"
#> [71] "chr22:17187665:TAA:TA"
#> [72] "chr22:17187665:TAA:TAAA"
#> [73] "chr22:17187977:G:GC"
#> [74] "chr22:17209889:AT:ATT"
#> [75] "chr22:17216769:AAAAC:ACAAAC"
#> [76] "chr22:17216770:AAAC:ACAAC"
#> [77] "chr22:17216771:A:AC"
#> [78] "chr22:17216771:C:A"
#> [79] "chr22:17216789:C:CACAT"
#> [80] "chr22:17216799:G:T"
#> [81] "chr22:17221295:GT:G"
#> [82] "chr22:17302680:G:A"
#> [83] "chr22:17303055:C:T"
#> [84] "chr22:17326841:T:C"
#> [85] "chr22:17327911:TACACAC:TACAC"
#> [86] "chr22:17331260:C:CT"
#> [87] "chr22:17350100:T:C"
#> [88] "chr22:17375405:A:G"
#> [89] "chr22:17379581:GGTGT:GGT"
#> [90] "chr22:17379581:GGTGT:GGTGTGT"
#> [91] "chr22:17379581:GGTGT:GGTGTGTGT"
#> [92] "chr22:17379581:GGTGT:GGTGTGTGTGT"
#> [93] "chr22:17427850:G:T"
#> [94] "chr22:17429117:G:A"
#> [95] "chr22:17449676:C:A"
#> [96] "chr22:17466675:G:T"
#> [97] "chr22:17469609:TCCAGTAAGAATCCAGTTCTC:TCAGTAAGAATCCAGTTCTC"
#> [98] "chr22:17469610:TCA:CCA"
#> [99] "chr22:17518422:C:T"
#> [100] "chr22:17523010:GAAAAA:AAAAAA"
#> [101] "chr22:17523010:GAAAAA:GA"
#> [102] "chr22:17577230:G:A"
#> [103] "chr22:17585626:ATTTATT:A"
#> [104] "chr22:17585630:ATT:*"
#> [105] "chr22:17658972:T:C"
#> [106] "chr22:17667743:T:A"
#> [107] "chr22:17683132:CA:C"
#> [108] "chr22:17683132:CA:CAAA"
#> [109] "chr22:17687818:CT:C"
#> [110] "chr22:17706998:A:G"
#> [111] "chr22:17721525:AT:ATTTTT"
#> [112] "chr22:17721525:ATTTT:AT"
#> [113] "chr22:17726847:G:A"
#> [114] "chr22:17734310:CTT:C"
#> [115] "chr22:17763207:A:G"
#> [116] "chr22:17765138:TCAAGACATCCTCCACAGAGGACC:T"
#> [117] "chr22:17768872:CAA:CA"
#> [118] "chr22:17768872:CAA:CAAA"
#> [119] "chr22:17839567:CTTT:CT"
#> [120] "chr22:17839567:CTTT:CTT"
#> [121] "chr22:17846396:T:TA"
#> [122] "chr22:17860245:C:A"
#> [123] "chr22:17876770:AGTTATGGAGGTTAGGGAGGTTAGGGAAGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTAGGGAG:GGTTATGGAGGTTAGGGAGGTTAGGGAAGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTAGGGAG"
#> [124] "chr22:17876799:TTATGGAGGTTAGGGAGGTTAG:*"
#> [125] "chr22:17876802:TGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTAG:*"
#> [126] "chr22:17876803:GGAGGTTAGGGAGGTTAGGGAGGTTAT:*"
#> [127] "chr22:17876805:AGGTT:*"
#> [128] "chr22:17876807:GTTA:*"
#> [129] "chr22:17876808:TTAGG:*"
#> [130] "chr22:17876810:AGGGAGGTTAGGGAG:*"
#> [131] "chr22:17879807:G:A"
#> [132] "chr22:17880174:G:A"
#> [133] "chr22:17898107:TAA:TA"
#> [134] "chr22:17898107:TAA:TAAA"
#> [135] "chr22:17929265:ATTTTTTTTT:ATTTTTT"
#> [136] "chr22:17929265:ATTTTTTTTT:ATTTTTTT"
#> [137] "chr22:17929265:ATTTTTTTTT:ATTTTTTTT"
#> [138] "chr22:17949102:C:T"
#> [139] "chr22:17955812:G:A"
#> [140] "chr22:17967486:A:ACACACACC"
#> [141] "chr22:17967486:A:ACACACC"
#> [142] "chr22:17967492:ACCCACACACACC:ACACACACACC"
#> [143] "chr22:17967494:C:*"
#> [144] "chr22:17977536:TA:TAA"
#> [145] "chr22:17998075:G:GTGAA"
#> [146] "chr22:18001877:A:C"
#> [147] "chr22:18064272:A:T"
#> [148] "chr22:18150441:CA:C"
#> [149] "chr22:18159414:A:G"
#> [150] "chr22:18160557:T:C"
#> [151] "chr22:18166484:T:TGA"
#> [152] "chr22:18173426:C:A"
#> [153] "chr22:18730960:GTATACATAAGATATATTATATATAATATATTATATAAATGTATTATATATAACATATTATATATAATATATT:*"
#> [154] "chr22:18731027:T:C"
#>
#> $region_data$chr22_2$z_gene
#> [1] id z type context group
#> <0 rows> (or 0-length row.names)
#>
#> $region_data$chr22_2$z_snp
#> id
#> 1 chr22:15574750:C:A
#> 2 chr22:15635104:C:A
#> 3 chr22:15689224:A:C
#> 4 chr22:15773180:G:A
#> 5 chr22:15837995:CTTTCTTTCTTTCTTTTTCTTT:CTTTTTCTTTCTTTCTTTTTCTTT
#> 6 chr22:15838001:TTCTTTCTTTTTCTTTC:TTTTCTTTTTCTTTC
#> 7 chr22:15838002:TCTTTCTTTTTCTTTCTTC:*
#> 8 chr22:15838003:CTTTCTTTTTCTTT:ATTTCTTTTTCTTT
#> 9 chr22:15838003:CTTTCTTTTTCTTT:CTTTTTCTTTTTCTTT
#> 10 chr22:15838010:TTTCTTTCTTCCTTCCTTCCTTCCTTCCTTCCTCCCTTCCTTC:TCTTCTTTCTTCCTTCCTTCCTTCCTTCCTTCCTCCCTTCCTTC
#> 11 chr22:15839920:G:A
#> 12 chr22:15919156:A:T
#> 13 chr22:15927084:C:T
#> 14 chr22:15947643:T:C
#> 15 chr22:15984722:T:C
#> 16 chr22:16073625:G:T
#> 17 chr22:16102937:C:T
#> 18 chr22:16111042:C:CA
#> 19 chr22:16112049:C:A
#> 20 chr22:16112091:TG:CG
#> 21 chr22:16115854:C:T
#> 22 chr22:16124912:C:T
#> 23 chr22:16132992:A:G
#> 24 chr22:16187126:A:G
#> 25 chr22:16207293:A:G
#> 26 chr22:16214693:C:A
#> 27 chr22:16217062:A:G
#> 28 chr22:16224528:T:C
#> 29 chr22:16234309:C:T
#> 30 chr22:16244919:T:C
#> 31 chr22:16254612:GGAAGGAAGGAAGGAAA:AGAAGGAAGGAAGGAAA
#> 32 chr22:16258960:C:A
#> 33 chr22:16262035:G:A
#> 34 chr22:16262334:GATTCCATTCGATGATTCCATTCA:G
#> 35 chr22:16262336:TTCCATTCGATGATTCCATTCAATTCCATTCGATGATGATTCCATTCGAG:*
#> 36 chr22:16262338:CCATTCGATGATTCCATTCAA:*
#> 37 chr22:16386749:TCCGCCGCCGCCGCGGCTTTTTGCCCCCCACCCCCGCCGCCGCGGCTTTTTACCCGCCGCGGCTTTTTGCCCCCCCGCCGCCGTGGTTTTTTCCCCCCATCTCACCTCCGCTTTTTGCCCGCCGCGGCTTTTTGCCCCCACCCCGCCTCGGCTTTTTGCCAGCCACGGCTTTTTGCCCCCCGCCACCGCGGCTTTTTGTCCC:*
#> 38 chr22:16386751:CGCCGCCGCCGCGGCTTTTTGCCCCCCACCCCCGCCGCCGCGGCTTTTTACCCGCCGCGGCTTTTTGCCCCCCCG:*
#> 39 chr22:16386752:GCCGCCGCCGCGGCTTTTTGCCCCCCACCCCCGCCGCCGCGGCTTTTTACCCGCCGCGGCTTTTTGCCCCCCCGCCGCCGTGGTTTTTTCCCCCCATCTCACCTCCGCTTTTTGCCCGCCGCGGCTTTTTGCCCCCACCCCGCCTCGGCTTTTTGCCAGCCACGGCTTTTTGCCCC:CCCGCCGCCGCGGCTTTTTGCCCCCCACCCCCGCCGCCGCGGCTTTTTACCCGCCGCGGCTTTTTGCCCCCCCGCCGCCGTGGTTTTTTCCCCCCATCTCACCTCCGCTTTTTGCCCGCCGCGGCTTTTTGCCCCCACCCCGCCTCGGCTTTTTGCCAGCCACGGCTTTTTGCCCC
#> 40 chr22:16400343:T:C
#> 41 chr22:16427771:T:C
#> 42 chr22:16439458:A:G
#> 43 chr22:16442170:G:A
#> 44 chr22:16549730:A:G
#> 45 chr22:16560460:ACAGCCAGCCAGCCAAGCCAGCCAAGCCAGCCAGGAAAGCCAGCCTGCCAAGCCAGCCAAGCCAGCCAGCCACTCAAGCCAGCCAAGTCAGCGAGCCAACCAAGCCAGCCAACTCAGCCAGCCACCTAAGCCAGCCAAGCCAGCCAGCCAGCCAAGCAAGCCAGCCAGCCAAGCCAGCCAAGCCAGCCAAGCCAGGCAGCCAGCCAAGCCAGCCAAGCCAGCCAGCCAGCCAAGCCAGCCAGCCAGCCCACACAGCCAAGC:*
#> 46 chr22:16560533:TCAAGCCAGCCAAGTCAGCGAGCCAACCAAGCCAGCCAACTCAGCCAGCCACCTAAGCCAGCCAAGCCAGCCAGCCAGCCAAGCAAGCCAGCCAGCCAAGCCAGCCAAGCCAGCCAAGCCAGGCAGCCAGC:CCAAGCCAGCCAAGTCAGCGAGCCAACCAAGCCAGCCAACTCAGCCAGCCACCTAAGCCAGCCAAGCCAGCCAGCCAGCCAAGCAAGCCAGCCAGCCAAGCCAGCCAAGCCAGCCAAGCCAGGCAGCCAGC
#> 47 chr22:16566547:ACAGCCAAGACAGCCAGCCAGCCACGCAAGCCAAGCCAGCCAGCCAGGCAAGCCAGGCATGCCAGCCAAGCCATCCAGCCAGCCAAGCCAGGCGGCCAGCCAAGCCAGCCAAGCCACCCGGCCAGCCAAGCCACCCAAGCCACCCGGCCAGCCAGGCATCCAAGCCAGCCAAGT:*
#> 48 chr22:16566742:CAAGCCAGCCAGCTAGCCAAGCCACCCAGCCAGCCAGCCAGCCAAACCAGCCAAGCCAGCCAGCCAGCCAGCCAAGCCAGCCAAGCAAGCCAGCCAGCCAGCCAAGCCACGCAAGCCAGCCAGCCAGCCATGCCAGCCA:TAAGCCAGCCAGCTAGCCAAGCCACCCAGCCAGCCAGCCAGCCAAACCAGCCAAGCCAGCCAGCCAGCCAGCCAAGCCAGCCAAGCAAGCCAGCCAGCCAGCCAAGCCACGCAAGCCAGCCAGCCAGCCATGCCAGCCA
#> 49 chr22:16841646:CAAAAAAAAAAAAAA:AAAAAAAAAAAAAAA
#> 50 chr22:16845585:TCA:TCACA
#> 51 chr22:16909478:TCTCTCC:*
#> 52 chr22:16909479:CTCTCCCTCTCTCTCTCTCTCTCTCCCT:CCCCTCTCTCTCTCTCTCTCTCCCT
#> 53 chr22:16909480:TCTCCCTCTCTCTCTCTCTCTCTCC:*
#> 54 chr22:16909481:CTCCCTCTCTCTCTCTCTCTCTCCCT:*
#> 55 chr22:16970638:G:A
#> 56 chr22:16973012:G:A
#> 57 chr22:17014255:C:T
#> 58 chr22:17051853:C:T
#> 59 chr22:17079499:GAAAAAAA:GAAAAAAAA
#> 60 chr22:17113082:AG:A
#> 61 chr22:17136539:C:T
#> 62 chr22:17154616:CTT:CTTT
#> 63 chr22:17154616:CTTT:CT
#> 64 chr22:17157085:TACACACAC:CACACACAC
#> 65 chr22:17157085:TACACACAC:T
#> 66 chr22:17157085:TACACACAC:TACACACACACACACAC
#> 67 chr22:17157085:TACACACAC:TACACACACACACACACACAC
#> 68 chr22:17157085:TACACACAC:TACACACACACACACACACACACAC
#> 69 chr22:17168884:C:T
#> 70 chr22:17172477:C:T
#> 71 chr22:17187665:TAA:TA
#> 72 chr22:17187665:TAA:TAAA
#> 73 chr22:17187977:G:GC
#> 74 chr22:17209889:AT:ATT
#> 75 chr22:17216769:AAAAC:ACAAAC
#> 76 chr22:17216770:AAAC:ACAAC
#> 77 chr22:17216771:A:AC
#> 78 chr22:17216771:C:A
#> 79 chr22:17216789:C:CACAT
#> 80 chr22:17216799:G:T
#> 81 chr22:17221295:GT:G
#> 82 chr22:17302680:G:A
#> 83 chr22:17303055:C:T
#> 84 chr22:17326841:T:C
#> 85 chr22:17327911:TACACAC:TACAC
#> 86 chr22:17331260:C:CT
#> 87 chr22:17350100:T:C
#> 88 chr22:17375405:A:G
#> 89 chr22:17379581:GGTGT:GGT
#> 90 chr22:17379581:GGTGT:GGTGTGT
#> 91 chr22:17379581:GGTGT:GGTGTGTGT
#> 92 chr22:17379581:GGTGT:GGTGTGTGTGT
#> 93 chr22:17427850:G:T
#> 94 chr22:17429117:G:A
#> 95 chr22:17449676:C:A
#> 96 chr22:17466675:G:T
#> 97 chr22:17469609:TCCAGTAAGAATCCAGTTCTC:TCAGTAAGAATCCAGTTCTC
#> 98 chr22:17469610:TCA:CCA
#> 99 chr22:17518422:C:T
#> 100 chr22:17523010:GAAAAA:AAAAAA
#> 101 chr22:17523010:GAAAAA:GA
#> 102 chr22:17577230:G:A
#> 103 chr22:17585626:ATTTATT:A
#> 104 chr22:17585630:ATT:*
#> 105 chr22:17658972:T:C
#> 106 chr22:17667743:T:A
#> 107 chr22:17683132:CA:C
#> 108 chr22:17683132:CA:CAAA
#> 109 chr22:17687818:CT:C
#> 110 chr22:17706998:A:G
#> 111 chr22:17721525:AT:ATTTTT
#> 112 chr22:17721525:ATTTT:AT
#> 113 chr22:17726847:G:A
#> 114 chr22:17734310:CTT:C
#> 115 chr22:17763207:A:G
#> 116 chr22:17765138:TCAAGACATCCTCCACAGAGGACC:T
#> 117 chr22:17768872:CAA:CA
#> 118 chr22:17768872:CAA:CAAA
#> 119 chr22:17839567:CTTT:CT
#> 120 chr22:17839567:CTTT:CTT
#> 121 chr22:17846396:T:TA
#> 122 chr22:17860245:C:A
#> 123 chr22:17876770:AGTTATGGAGGTTAGGGAGGTTAGGGAAGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTAGGGAG:GGTTATGGAGGTTAGGGAGGTTAGGGAAGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTAGGGAG
#> 124 chr22:17876799:TTATGGAGGTTAGGGAGGTTAG:*
#> 125 chr22:17876802:TGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTAG:*
#> 126 chr22:17876803:GGAGGTTAGGGAGGTTAGGGAGGTTAT:*
#> 127 chr22:17876805:AGGTT:*
#> 128 chr22:17876807:GTTA:*
#> 129 chr22:17876808:TTAGG:*
#> 130 chr22:17876810:AGGGAGGTTAGGGAG:*
#> 131 chr22:17879807:G:A
#> 132 chr22:17880174:G:A
#> 133 chr22:17898107:TAA:TA
#> 134 chr22:17898107:TAA:TAAA
#> 135 chr22:17929265:ATTTTTTTTT:ATTTTTT
#> 136 chr22:17929265:ATTTTTTTTT:ATTTTTTT
#> 137 chr22:17929265:ATTTTTTTTT:ATTTTTTTT
#> 138 chr22:17949102:C:T
#> 139 chr22:17955812:G:A
#> 140 chr22:17967486:A:ACACACACC
#> 141 chr22:17967486:A:ACACACC
#> 142 chr22:17967492:ACCCACACACACC:ACACACACACC
#> 143 chr22:17967494:C:*
#> 144 chr22:17977536:TA:TAA
#> 145 chr22:17998075:G:GTGAA
#> 146 chr22:18001877:A:C
#> 147 chr22:18064272:A:T
#> 148 chr22:18150441:CA:C
#> 149 chr22:18159414:A:G
#> 150 chr22:18160557:T:C
#> 151 chr22:18166484:T:TGA
#> 152 chr22:18173426:C:A
#> 153 chr22:18730960:GTATACATAAGATATATTATATATAATATATTATATAAATGTATTATATATAACATATTATATATAATATATT:*
#> 154 chr22:18731027:T:C
#> z type context group
#> 1 -0.369669557 SNP SNP SNP
#> 2 2.060093786 SNP SNP SNP
#> 3 -1.365424594 SNP SNP SNP
#> 4 -0.879863066 SNP SNP SNP
#> 5 1.302031888 SNP SNP SNP
#> 6 -0.940937683 SNP SNP SNP
#> 7 0.487766437 SNP SNP SNP
#> 8 -0.768355209 SNP SNP SNP
#> 9 0.475296689 SNP SNP SNP
#> 10 -0.736066147 SNP SNP SNP
#> 11 -0.962992675 SNP SNP SNP
#> 12 0.099933461 SNP SNP SNP
#> 13 2.554708301 SNP SNP SNP
#> 14 -0.390380768 SNP SNP SNP
#> 15 0.480652000 SNP SNP SNP
#> 16 1.328106597 SNP SNP SNP
#> 17 -2.498801748 SNP SNP SNP
#> 18 -0.353758398 SNP SNP SNP
#> 19 -0.891881582 SNP SNP SNP
#> 20 3.017911741 SNP SNP SNP
#> 21 0.470594294 SNP SNP SNP
#> 22 -0.959004494 SNP SNP SNP
#> 23 0.754848901 SNP SNP SNP
#> 24 -1.855905901 SNP SNP SNP
#> 25 0.864983545 SNP SNP SNP
#> 26 -0.368226737 SNP SNP SNP
#> 27 0.925424807 SNP SNP SNP
#> 28 0.826528152 SNP SNP SNP
#> 29 -0.746489583 SNP SNP SNP
#> 30 -0.443852792 SNP SNP SNP
#> 31 0.622144483 SNP SNP SNP
#> 32 2.140633275 SNP SNP SNP
#> 33 1.672167723 SNP SNP SNP
#> 34 0.450538420 SNP SNP SNP
#> 35 -0.922381817 SNP SNP SNP
#> 36 0.970297129 SNP SNP SNP
#> 37 0.314798746 SNP SNP SNP
#> 38 -1.107864073 SNP SNP SNP
#> 39 -0.960195073 SNP SNP SNP
#> 40 -0.760341925 SNP SNP SNP
#> 41 0.724376860 SNP SNP SNP
#> 42 -0.006873117 SNP SNP SNP
#> 43 0.881847048 SNP SNP SNP
#> 44 3.062602156 SNP SNP SNP
#> 45 0.343962121 SNP SNP SNP
#> 46 -1.712041364 SNP SNP SNP
#> 47 0.803583107 SNP SNP SNP
#> 48 -0.574844760 SNP SNP SNP
#> 49 -0.498219437 SNP SNP SNP
#> 50 4.131720803 SNP SNP SNP
#> 51 -0.222876318 SNP SNP SNP
#> 52 0.381879731 SNP SNP SNP
#> 53 1.049286103 SNP SNP SNP
#> 54 0.555251420 SNP SNP SNP
#> 55 -1.545294462 SNP SNP SNP
#> 56 0.447633421 SNP SNP SNP
#> 57 -0.756971150 SNP SNP SNP
#> 58 -2.230811748 SNP SNP SNP
#> 59 -0.725056455 SNP SNP SNP
#> 60 -0.024204349 SNP SNP SNP
#> 61 0.471999922 SNP SNP SNP
#> 62 -2.737633939 SNP SNP SNP
#> 63 -0.365189998 SNP SNP SNP
#> 64 -0.779549150 SNP SNP SNP
#> 65 2.288184108 SNP SNP SNP
#> 66 2.562341769 SNP SNP SNP
#> 67 1.342007543 SNP SNP SNP
#> 68 0.466882112 SNP SNP SNP
#> 69 0.003271000 SNP SNP SNP
#> 70 -0.225474759 SNP SNP SNP
#> 71 -1.537687049 SNP SNP SNP
#> 72 -2.248287061 SNP SNP SNP
#> 73 1.074911790 SNP SNP SNP
#> 74 3.107043981 SNP SNP SNP
#> 75 0.280600944 SNP SNP SNP
#> 76 -0.759671951 SNP SNP SNP
#> 77 1.085673279 SNP SNP SNP
#> 78 0.521613583 SNP SNP SNP
#> 79 0.684947689 SNP SNP SNP
#> 80 -1.260535702 SNP SNP SNP
#> 81 0.143854906 SNP SNP SNP
#> 82 -0.481471483 SNP SNP SNP
#> 83 -1.932355374 SNP SNP SNP
#> 84 -2.023208819 SNP SNP SNP
#> 85 -2.164319369 SNP SNP SNP
#> 86 -0.995977717 SNP SNP SNP
#> 87 1.366754672 SNP SNP SNP
#> 88 -0.864920932 SNP SNP SNP
#> 89 -0.202001942 SNP SNP SNP
#> 90 -0.674890563 SNP SNP SNP
#> 91 -0.416038223 SNP SNP SNP
#> 92 -0.624174109 SNP SNP SNP
#> 93 -0.027015339 SNP SNP SNP
#> 94 -0.535601768 SNP SNP SNP
#> 95 -0.135411084 SNP SNP SNP
#> 96 -0.379613534 SNP SNP SNP
#> 97 -0.369349174 SNP SNP SNP
#> 98 -0.356709741 SNP SNP SNP
#> 99 1.839641160 SNP SNP SNP
#> 100 -0.472479028 SNP SNP SNP
#> 101 1.459281515 SNP SNP SNP
#> 102 6.789288191 SNP SNP SNP
#> 103 0.043790821 SNP SNP SNP
#> 104 0.969675074 SNP SNP SNP
#> 105 -1.884907755 SNP SNP SNP
#> 106 -1.212161942 SNP SNP SNP
#> 107 4.020978730 SNP SNP SNP
#> 108 -2.260093565 SNP SNP SNP
#> 109 1.199758325 SNP SNP SNP
#> 110 -0.708022102 SNP SNP SNP
#> 111 2.571985029 SNP SNP SNP
#> 112 1.022171031 SNP SNP SNP
#> 113 0.839967121 SNP SNP SNP
#> 114 -0.173360563 SNP SNP SNP
#> 115 -1.873758505 SNP SNP SNP
#> 116 -2.676356303 SNP SNP SNP
#> 117 3.292765803 SNP SNP SNP
#> 118 -0.667248777 SNP SNP SNP
#> 119 0.132170273 SNP SNP SNP
#> 120 -2.805484334 SNP SNP SNP
#> 121 -0.771035998 SNP SNP SNP
#> 122 1.736401755 SNP SNP SNP
#> 123 0.015668485 SNP SNP SNP
#> 124 0.366082733 SNP SNP SNP
#> 125 0.287701865 SNP SNP SNP
#> 126 -0.761724577 SNP SNP SNP
#> 127 -1.554413489 SNP SNP SNP
#> 128 -0.294052435 SNP SNP SNP
#> 129 0.431650231 SNP SNP SNP
#> 130 -1.477727803 SNP SNP SNP
#> 131 2.062125671 SNP SNP SNP
#> 132 -1.099305382 SNP SNP SNP
#> 133 0.495291129 SNP SNP SNP
#> 134 1.242328888 SNP SNP SNP
#> 135 1.255709137 SNP SNP SNP
#> 136 0.121123862 SNP SNP SNP
#> 137 -0.068983875 SNP SNP SNP
#> 138 -0.427370355 SNP SNP SNP
#> 139 -0.516884295 SNP SNP SNP
#> 140 -2.664396295 SNP SNP SNP
#> 141 -0.324681850 SNP SNP SNP
#> 142 1.145269644 SNP SNP SNP
#> 143 1.382946720 SNP SNP SNP
#> 144 3.268483767 SNP SNP SNP
#> 145 2.826239506 SNP SNP SNP
#> 146 -1.805260705 SNP SNP SNP
#> 147 1.467859008 SNP SNP SNP
#> 148 -0.794067434 SNP SNP SNP
#> 149 -1.124449470 SNP SNP SNP
#> 150 3.398057020 SNP SNP SNP
#> 151 -1.274528490 SNP SNP SNP
#> 152 0.325268398 SNP SNP SNP
#> 153 0.843093142 SNP SNP SNP
#> 154 -1.469343859 SNP SNP SNP
#>
#> $region_data$chr22_2$types
#> [1] "SNP"
#>
#> $region_data$chr22_2$contexts
#> [1] "SNP"
#>
#> $region_data$chr22_2$groups
#> [1] "SNP"
#>
#>
#>
#> $boundary_genes
#> chrom p0 p1
#> 1 22 10685239 18850784
#> id molecular_id
#> 1 chr22_1|protocol_example|bulk_rnaseq|ENSG00000130538|susie ENSG00000130538
#> region_start region_stop region_id n_regions
#> 1 10685239 18850784 chr22_1,chr22_2 2
#>
#> $screen_res
#> $screen_res$screened_region_data
#> NULL
#>
#> $screen_res$screen_summary
#> region_id n_gids n_sids max_gene_absZ max_snp_absZ min_gene_p min_snp_p
#> 1 chr22_1 1 19 1.826089 2.933840 0.06783685 3.347966e-03
#> 2 chr22_2 0 154 NA 6.789288 NA 1.126881e-11
#> nonSNP_PIP
#> 1 0.01256304
#> 2 NA
#>
#>
#> $region_info
#> region_id chrom start stop
#> 1 chr22_1 22 10685239 12640661
#> 2 chr22_2 22 15574750 18850784
#>
#> $z_snp
#> id
#> 1 chr22:10685239:C:T
#> 2 chr22:10761227:G:A
#> 3 chr22:11285239:C:T
#> 4 chr22:11601805:G:A
#> 5 chr22:11791698:G:T
#> 6 chr22:11797697:C:T
#> 7 chr22:12044872:A:C
#> 8 chr22:12194389:G:A
#> 9 chr22:12207043:C:T
#> 10 chr22:12350816:G:A
#> 11 chr22:12352464:C:A
#> 12 chr22:12370627:C:T
#> 13 chr22:12383838:G:A
#> 14 chr22:12571373:AGAAAGAAAGAAAGAAAGAAG:*
#> 15 chr22:12571377:AGAAAGAAAGAAAGAAG:*
#> 16 chr22:12571385:AGAAAGAAG:*
#> 17 chr22:12571386:GAAAGAAGGA:*
#> 18 chr22:12571389:AGAAGGAAAGAAGGAAAGAAAGGAAGAAGGAAAGAAG:*
#> 19 chr22:12576050:T:A
#> 20 chr22:12640661:G:T
#> 21 chr22:15574750:C:A
#> 22 chr22:15635104:C:A
#> 23 chr22:15689224:A:C
#> 24 chr22:15773180:G:A
#> 25 chr22:15837995:CTTTCTTTCTTTCTTTTTCTTT:CTTTTTCTTTCTTTCTTTTTCTTT
#> 26 chr22:15838001:TTCTTTCTTTTTCTTTC:TTTTCTTTTTCTTTC
#> 27 chr22:15838002:TCTTTCTTTTTCTTTCTTC:*
#> 28 chr22:15838003:CTTTCTTTTTCTTT:ATTTCTTTTTCTTT
#> 29 chr22:15838003:CTTTCTTTTTCTTT:CTTTTTCTTTTTCTTT
#> 30 chr22:15838010:TTTCTTTCTTCCTTCCTTCCTTCCTTCCTTCCTCCCTTCCTTC:TCTTCTTTCTTCCTTCCTTCCTTCCTTCCTTCCTCCCTTCCTTC
#> 31 chr22:15839920:G:A
#> 32 chr22:15919156:A:T
#> 33 chr22:15927084:C:T
#> 34 chr22:15947643:T:C
#> 35 chr22:15984722:T:C
#> 36 chr22:16073625:G:T
#> 37 chr22:16102937:C:T
#> 38 chr22:16111042:C:CA
#> 39 chr22:16112049:C:A
#> 40 chr22:16112091:TG:CG
#> 41 chr22:16115854:C:T
#> 42 chr22:16124912:C:T
#> 43 chr22:16132992:A:G
#> 44 chr22:16187126:A:G
#> 45 chr22:16207293:A:G
#> 46 chr22:16214693:C:A
#> 47 chr22:16217062:A:G
#> 48 chr22:16224528:T:C
#> 49 chr22:16234309:C:T
#> 50 chr22:16244919:T:C
#> 51 chr22:16254612:GGAAGGAAGGAAGGAAA:AGAAGGAAGGAAGGAAA
#> 52 chr22:16258960:C:A
#> 53 chr22:16262035:G:A
#> 54 chr22:16262334:GATTCCATTCGATGATTCCATTCA:G
#> 55 chr22:16262336:TTCCATTCGATGATTCCATTCAATTCCATTCGATGATGATTCCATTCGAG:*
#> 56 chr22:16262338:CCATTCGATGATTCCATTCAA:*
#> 57 chr22:16386749:TCCGCCGCCGCCGCGGCTTTTTGCCCCCCACCCCCGCCGCCGCGGCTTTTTACCCGCCGCGGCTTTTTGCCCCCCCGCCGCCGTGGTTTTTTCCCCCCATCTCACCTCCGCTTTTTGCCCGCCGCGGCTTTTTGCCCCCACCCCGCCTCGGCTTTTTGCCAGCCACGGCTTTTTGCCCCCCGCCACCGCGGCTTTTTGTCCC:*
#> 58 chr22:16386751:CGCCGCCGCCGCGGCTTTTTGCCCCCCACCCCCGCCGCCGCGGCTTTTTACCCGCCGCGGCTTTTTGCCCCCCCG:*
#> 59 chr22:16386752:GCCGCCGCCGCGGCTTTTTGCCCCCCACCCCCGCCGCCGCGGCTTTTTACCCGCCGCGGCTTTTTGCCCCCCCGCCGCCGTGGTTTTTTCCCCCCATCTCACCTCCGCTTTTTGCCCGCCGCGGCTTTTTGCCCCCACCCCGCCTCGGCTTTTTGCCAGCCACGGCTTTTTGCCCC:CCCGCCGCCGCGGCTTTTTGCCCCCCACCCCCGCCGCCGCGGCTTTTTACCCGCCGCGGCTTTTTGCCCCCCCGCCGCCGTGGTTTTTTCCCCCCATCTCACCTCCGCTTTTTGCCCGCCGCGGCTTTTTGCCCCCACCCCGCCTCGGCTTTTTGCCAGCCACGGCTTTTTGCCCC
#> 60 chr22:16400343:T:C
#> 61 chr22:16427771:T:C
#> 62 chr22:16439458:A:G
#> 63 chr22:16442170:G:A
#> 64 chr22:16549730:A:G
#> 65 chr22:16560460:ACAGCCAGCCAGCCAAGCCAGCCAAGCCAGCCAGGAAAGCCAGCCTGCCAAGCCAGCCAAGCCAGCCAGCCACTCAAGCCAGCCAAGTCAGCGAGCCAACCAAGCCAGCCAACTCAGCCAGCCACCTAAGCCAGCCAAGCCAGCCAGCCAGCCAAGCAAGCCAGCCAGCCAAGCCAGCCAAGCCAGCCAAGCCAGGCAGCCAGCCAAGCCAGCCAAGCCAGCCAGCCAGCCAAGCCAGCCAGCCAGCCCACACAGCCAAGC:*
#> 66 chr22:16560533:TCAAGCCAGCCAAGTCAGCGAGCCAACCAAGCCAGCCAACTCAGCCAGCCACCTAAGCCAGCCAAGCCAGCCAGCCAGCCAAGCAAGCCAGCCAGCCAAGCCAGCCAAGCCAGCCAAGCCAGGCAGCCAGC:CCAAGCCAGCCAAGTCAGCGAGCCAACCAAGCCAGCCAACTCAGCCAGCCACCTAAGCCAGCCAAGCCAGCCAGCCAGCCAAGCAAGCCAGCCAGCCAAGCCAGCCAAGCCAGCCAAGCCAGGCAGCCAGC
#> 67 chr22:16566547:ACAGCCAAGACAGCCAGCCAGCCACGCAAGCCAAGCCAGCCAGCCAGGCAAGCCAGGCATGCCAGCCAAGCCATCCAGCCAGCCAAGCCAGGCGGCCAGCCAAGCCAGCCAAGCCACCCGGCCAGCCAAGCCACCCAAGCCACCCGGCCAGCCAGGCATCCAAGCCAGCCAAGT:*
#> 68 chr22:16566742:CAAGCCAGCCAGCTAGCCAAGCCACCCAGCCAGCCAGCCAGCCAAACCAGCCAAGCCAGCCAGCCAGCCAGCCAAGCCAGCCAAGCAAGCCAGCCAGCCAGCCAAGCCACGCAAGCCAGCCAGCCAGCCATGCCAGCCA:TAAGCCAGCCAGCTAGCCAAGCCACCCAGCCAGCCAGCCAGCCAAACCAGCCAAGCCAGCCAGCCAGCCAGCCAAGCCAGCCAAGCAAGCCAGCCAGCCAGCCAAGCCACGCAAGCCAGCCAGCCAGCCATGCCAGCCA
#> 69 chr22:16841646:CAAAAAAAAAAAAAA:AAAAAAAAAAAAAAA
#> 70 chr22:16845585:TCA:TCACA
#> 71 chr22:16909478:TCTCTCC:*
#> 72 chr22:16909479:CTCTCCCTCTCTCTCTCTCTCTCTCCCT:CCCCTCTCTCTCTCTCTCTCTCCCT
#> 73 chr22:16909480:TCTCCCTCTCTCTCTCTCTCTCTCC:*
#> 74 chr22:16909481:CTCCCTCTCTCTCTCTCTCTCTCCCT:*
#> 75 chr22:16970638:G:A
#> 76 chr22:16973012:G:A
#> 77 chr22:17014255:C:T
#> 78 chr22:17051853:C:T
#> 79 chr22:17079499:GAAAAAAA:GAAAAAAAA
#> 80 chr22:17113082:AG:A
#> 81 chr22:17136539:C:T
#> 82 chr22:17154616:CTT:CTTT
#> 83 chr22:17154616:CTTT:CT
#> 84 chr22:17157085:TACACACAC:CACACACAC
#> 85 chr22:17157085:TACACACAC:T
#> 86 chr22:17157085:TACACACAC:TACACACACACACACAC
#> 87 chr22:17157085:TACACACAC:TACACACACACACACACACAC
#> 88 chr22:17157085:TACACACAC:TACACACACACACACACACACACAC
#> 89 chr22:17168884:C:T
#> 90 chr22:17172477:C:T
#> 91 chr22:17187665:TAA:TA
#> 92 chr22:17187665:TAA:TAAA
#> 93 chr22:17187977:G:GC
#> 94 chr22:17209889:AT:ATT
#> 95 chr22:17216769:AAAAC:ACAAAC
#> 96 chr22:17216770:AAAC:ACAAC
#> 97 chr22:17216771:A:AC
#> 98 chr22:17216771:C:A
#> 99 chr22:17216789:C:CACAT
#> 100 chr22:17216799:G:T
#> 101 chr22:17221295:GT:G
#> 102 chr22:17302680:G:A
#> 103 chr22:17303055:C:T
#> 104 chr22:17326841:T:C
#> 105 chr22:17327911:TACACAC:TACAC
#> 106 chr22:17331260:C:CT
#> 107 chr22:17350100:T:C
#> 108 chr22:17375405:A:G
#> 109 chr22:17379581:GGTGT:GGT
#> 110 chr22:17379581:GGTGT:GGTGTGT
#> 111 chr22:17379581:GGTGT:GGTGTGTGT
#> 112 chr22:17379581:GGTGT:GGTGTGTGTGT
#> 113 chr22:17427850:G:T
#> 114 chr22:17429117:G:A
#> 115 chr22:17449676:C:A
#> 116 chr22:17466675:G:T
#> 117 chr22:17469609:TCCAGTAAGAATCCAGTTCTC:TCAGTAAGAATCCAGTTCTC
#> 118 chr22:17469610:TCA:CCA
#> 119 chr22:17518422:C:T
#> 120 chr22:17523010:GAAAAA:AAAAAA
#> 121 chr22:17523010:GAAAAA:GA
#> 122 chr22:17577230:G:A
#> 123 chr22:17585626:ATTTATT:A
#> 124 chr22:17585630:ATT:*
#> 125 chr22:17658972:T:C
#> 126 chr22:17667743:T:A
#> 127 chr22:17683132:CA:C
#> 128 chr22:17683132:CA:CAAA
#> 129 chr22:17687818:CT:C
#> 130 chr22:17706998:A:G
#> 131 chr22:17721525:AT:ATTTTT
#> 132 chr22:17721525:ATTTT:AT
#> 133 chr22:17726847:G:A
#> 134 chr22:17734310:CTT:C
#> 135 chr22:17763207:A:G
#> 136 chr22:17765138:TCAAGACATCCTCCACAGAGGACC:T
#> 137 chr22:17768872:CAA:CA
#> 138 chr22:17768872:CAA:CAAA
#> 139 chr22:17839567:CTTT:CT
#> 140 chr22:17839567:CTTT:CTT
#> 141 chr22:17846396:T:TA
#> 142 chr22:17860245:C:A
#> 143 chr22:17876770:AGTTATGGAGGTTAGGGAGGTTAGGGAAGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTAGGGAG:GGTTATGGAGGTTAGGGAGGTTAGGGAAGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTAGGGAG
#> 144 chr22:17876799:TTATGGAGGTTAGGGAGGTTAG:*
#> 145 chr22:17876802:TGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTAG:*
#> 146 chr22:17876803:GGAGGTTAGGGAGGTTAGGGAGGTTAT:*
#> 147 chr22:17876805:AGGTT:*
#> 148 chr22:17876807:GTTA:*
#> 149 chr22:17876808:TTAGG:*
#> 150 chr22:17876810:AGGGAGGTTAGGGAG:*
#> 151 chr22:17879807:G:A
#> 152 chr22:17880174:G:A
#> 153 chr22:17898107:TAA:TA
#> 154 chr22:17898107:TAA:TAAA
#> 155 chr22:17929265:ATTTTTTTTT:ATTTTTT
#> 156 chr22:17929265:ATTTTTTTTT:ATTTTTTT
#> 157 chr22:17929265:ATTTTTTTTT:ATTTTTTTT
#> 158 chr22:17949102:C:T
#> 159 chr22:17955812:G:A
#> 160 chr22:17967486:A:ACACACACC
#> 161 chr22:17967486:A:ACACACC
#> 162 chr22:17967492:ACCCACACACACC:ACACACACACC
#> 163 chr22:17967494:C:*
#> 164 chr22:17977536:TA:TAA
#> 165 chr22:17998075:G:GTGAA
#> 166 chr22:18001877:A:C
#> 167 chr22:18064272:A:T
#> 168 chr22:18150441:CA:C
#> 169 chr22:18159414:A:G
#> 170 chr22:18160557:T:C
#> 171 chr22:18166484:T:TGA
#> 172 chr22:18173426:C:A
#> 173 chr22:18730960:GTATACATAAGATATATTATATATAATATATTATATAAATGTATTATATATAACATATTATATATAATATATT:*
#> 174 chr22:18731027:T:C
#> 175 chr22:18850784:T:G
#> chrom pos
#> 1 22 10685239
#> 2 22 10761227
#> 3 22 11285239
#> 4 22 11601805
#> 5 22 11791698
#> 6 22 11797697
#> 7 22 12044872
#> 8 22 12194389
#> 9 22 12207043
#> 10 22 12350816
#> 11 22 12352464
#> 12 22 12370627
#> 13 22 12383838
#> 14 22 12571373
#> 15 22 12571377
#> 16 22 12571385
#> 17 22 12571386
#> 18 22 12571389
#> 19 22 12576050
#> 20 22 12640661
#> 21 22 15574750
#> 22 22 15635104
#> 23 22 15689224
#> 24 22 15773180
#> 25 22 15837995
#> 26 22 15838001
#> 27 22 15838002
#> 28 22 15838003
#> 29 22 15838003
#> 30 22 15838010
#> 31 22 15839920
#> 32 22 15919156
#> 33 22 15927084
#> 34 22 15947643
#> 35 22 15984722
#> 36 22 16073625
#> 37 22 16102937
#> 38 22 16111042
#> 39 22 16112049
#> 40 22 16112091
#> 41 22 16115854
#> 42 22 16124912
#> 43 22 16132992
#> 44 22 16187126
#> 45 22 16207293
#> 46 22 16214693
#> 47 22 16217062
#> 48 22 16224528
#> 49 22 16234309
#> 50 22 16244919
#> 51 22 16254612
#> 52 22 16258960
#> 53 22 16262035
#> 54 22 16262334
#> 55 22 16262336
#> 56 22 16262338
#> 57 22 16386749
#> 58 22 16386751
#> 59 22 16386752
#> 60 22 16400343
#> 61 22 16427771
#> 62 22 16439458
#> 63 22 16442170
#> 64 22 16549730
#> 65 22 16560460
#> 66 22 16560533
#> 67 22 16566547
#> 68 22 16566742
#> 69 22 16841646
#> 70 22 16845585
#> 71 22 16909478
#> 72 22 16909479
#> 73 22 16909480
#> 74 22 16909481
#> 75 22 16970638
#> 76 22 16973012
#> 77 22 17014255
#> 78 22 17051853
#> 79 22 17079499
#> 80 22 17113082
#> 81 22 17136539
#> 82 22 17154616
#> 83 22 17154616
#> 84 22 17157085
#> 85 22 17157085
#> 86 22 17157085
#> 87 22 17157085
#> 88 22 17157085
#> 89 22 17168884
#> 90 22 17172477
#> 91 22 17187665
#> 92 22 17187665
#> 93 22 17187977
#> 94 22 17209889
#> 95 22 17216769
#> 96 22 17216770
#> 97 22 17216771
#> 98 22 17216771
#> 99 22 17216789
#> 100 22 17216799
#> 101 22 17221295
#> 102 22 17302680
#> 103 22 17303055
#> 104 22 17326841
#> 105 22 17327911
#> 106 22 17331260
#> 107 22 17350100
#> 108 22 17375405
#> 109 22 17379581
#> 110 22 17379581
#> 111 22 17379581
#> 112 22 17379581
#> 113 22 17427850
#> 114 22 17429117
#> 115 22 17449676
#> 116 22 17466675
#> 117 22 17469609
#> 118 22 17469610
#> 119 22 17518422
#> 120 22 17523010
#> 121 22 17523010
#> 122 22 17577230
#> 123 22 17585626
#> 124 22 17585630
#> 125 22 17658972
#> 126 22 17667743
#> 127 22 17683132
#> 128 22 17683132
#> 129 22 17687818
#> 130 22 17706998
#> 131 22 17721525
#> 132 22 17721525
#> 133 22 17726847
#> 134 22 17734310
#> 135 22 17763207
#> 136 22 17765138
#> 137 22 17768872
#> 138 22 17768872
#> 139 22 17839567
#> 140 22 17839567
#> 141 22 17846396
#> 142 22 17860245
#> 143 22 17876770
#> 144 22 17876799
#> 145 22 17876802
#> 146 22 17876803
#> 147 22 17876805
#> 148 22 17876807
#> 149 22 17876808
#> 150 22 17876810
#> 151 22 17879807
#> 152 22 17880174
#> 153 22 17898107
#> 154 22 17898107
#> 155 22 17929265
#> 156 22 17929265
#> 157 22 17929265
#> 158 22 17949102
#> 159 22 17955812
#> 160 22 17967486
#> 161 22 17967486
#> 162 22 17967492
#> 163 22 17967494
#> 164 22 17977536
#> 165 22 17998075
#> 166 22 18001877
#> 167 22 18064272
#> 168 22 18150441
#> 169 22 18159414
#> 170 22 18160557
#> 171 22 18166484
#> 172 22 18173426
#> 173 22 18730960
#> 174 22 18731027
#> 175 22 18850784
#> A1
#> 1 T
#> 2 A
#> 3 T
#> 4 A
#> 5 T
#> 6 T
#> 7 C
#> 8 A
#> 9 T
#> 10 A
#> 11 A
#> 12 T
#> 13 A
#> 14 *
#> 15 *
#> 16 *
#> 17 *
#> 18 *
#> 19 A
#> 20 T
#> 21 A
#> 22 A
#> 23 C
#> 24 A
#> 25 CTTTTTCTTTCTTTCTTTTTCTTT
#> 26 TTTTCTTTTTCTTTC
#> 27 *
#> 28 ATTTCTTTTTCTTT
#> 29 CTTTTTCTTTTTCTTT
#> 30 TCTTCTTTCTTCCTTCCTTCCTTCCTTCCTTCCTCCCTTCCTTC
#> 31 A
#> 32 T
#> 33 T
#> 34 C
#> 35 C
#> 36 T
#> 37 T
#> 38 CA
#> 39 A
#> 40 CG
#> 41 T
#> 42 T
#> 43 G
#> 44 G
#> 45 G
#> 46 A
#> 47 G
#> 48 C
#> 49 T
#> 50 C
#> 51 AGAAGGAAGGAAGGAAA
#> 52 A
#> 53 A
#> 54 G
#> 55 *
#> 56 *
#> 57 *
#> 58 *
#> 59 CCCGCCGCCGCGGCTTTTTGCCCCCCACCCCCGCCGCCGCGGCTTTTTACCCGCCGCGGCTTTTTGCCCCCCCGCCGCCGTGGTTTTTTCCCCCCATCTCACCTCCGCTTTTTGCCCGCCGCGGCTTTTTGCCCCCACCCCGCCTCGGCTTTTTGCCAGCCACGGCTTTTTGCCCC
#> 60 C
#> 61 C
#> 62 G
#> 63 A
#> 64 G
#> 65 *
#> 66 CCAAGCCAGCCAAGTCAGCGAGCCAACCAAGCCAGCCAACTCAGCCAGCCACCTAAGCCAGCCAAGCCAGCCAGCCAGCCAAGCAAGCCAGCCAGCCAAGCCAGCCAAGCCAGCCAAGCCAGGCAGCCAGC
#> 67 *
#> 68 TAAGCCAGCCAGCTAGCCAAGCCACCCAGCCAGCCAGCCAGCCAAACCAGCCAAGCCAGCCAGCCAGCCAGCCAAGCCAGCCAAGCAAGCCAGCCAGCCAGCCAAGCCACGCAAGCCAGCCAGCCAGCCATGCCAGCCA
#> 69 AAAAAAAAAAAAAAA
#> 70 TCACA
#> 71 *
#> 72 CCCCTCTCTCTCTCTCTCTCTCCCT
#> 73 *
#> 74 *
#> 75 A
#> 76 A
#> 77 T
#> 78 T
#> 79 GAAAAAAAA
#> 80 A
#> 81 T
#> 82 CTTT
#> 83 CT
#> 84 CACACACAC
#> 85 T
#> 86 TACACACACACACACAC
#> 87 TACACACACACACACACACAC
#> 88 TACACACACACACACACACACACAC
#> 89 T
#> 90 T
#> 91 TA
#> 92 TAAA
#> 93 GC
#> 94 ATT
#> 95 ACAAAC
#> 96 ACAAC
#> 97 AC
#> 98 A
#> 99 CACAT
#> 100 T
#> 101 G
#> 102 A
#> 103 T
#> 104 C
#> 105 TACAC
#> 106 CT
#> 107 C
#> 108 G
#> 109 GGT
#> 110 GGTGTGT
#> 111 GGTGTGTGT
#> 112 GGTGTGTGTGT
#> 113 T
#> 114 A
#> 115 A
#> 116 T
#> 117 TCAGTAAGAATCCAGTTCTC
#> 118 CCA
#> 119 T
#> 120 AAAAAA
#> 121 GA
#> 122 A
#> 123 A
#> 124 *
#> 125 C
#> 126 A
#> 127 C
#> 128 CAAA
#> 129 C
#> 130 G
#> 131 ATTTTT
#> 132 AT
#> 133 A
#> 134 C
#> 135 G
#> 136 T
#> 137 CA
#> 138 CAAA
#> 139 CT
#> 140 CTT
#> 141 TA
#> 142 A
#> 143 GGTTATGGAGGTTAGGGAGGTTAGGGAAGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTAGGGAG
#> 144 *
#> 145 *
#> 146 *
#> 147 *
#> 148 *
#> 149 *
#> 150 *
#> 151 A
#> 152 A
#> 153 TA
#> 154 TAAA
#> 155 ATTTTTT
#> 156 ATTTTTTT
#> 157 ATTTTTTTT
#> 158 T
#> 159 A
#> 160 ACACACACC
#> 161 ACACACC
#> 162 ACACACACACC
#> 163 *
#> 164 TAA
#> 165 GTGAA
#> 166 C
#> 167 T
#> 168 C
#> 169 G
#> 170 C
#> 171 TGA
#> 172 A
#> 173 *
#> 174 C
#> 175 G
#> A2
#> 1 C
#> 2 G
#> 3 C
#> 4 G
#> 5 G
#> 6 C
#> 7 A
#> 8 G
#> 9 C
#> 10 G
#> 11 C
#> 12 C
#> 13 G
#> 14 AGAAAGAAAGAAAGAAAGAAG
#> 15 AGAAAGAAAGAAAGAAG
#> 16 AGAAAGAAG
#> 17 GAAAGAAGGA
#> 18 AGAAGGAAAGAAGGAAAGAAAGGAAGAAGGAAAGAAG
#> 19 T
#> 20 G
#> 21 C
#> 22 C
#> 23 A
#> 24 G
#> 25 CTTTCTTTCTTTCTTTTTCTTT
#> 26 TTCTTTCTTTTTCTTTC
#> 27 TCTTTCTTTTTCTTTCTTC
#> 28 CTTTCTTTTTCTTT
#> 29 CTTTCTTTTTCTTT
#> 30 TTTCTTTCTTCCTTCCTTCCTTCCTTCCTTCCTCCCTTCCTTC
#> 31 G
#> 32 A
#> 33 C
#> 34 T
#> 35 T
#> 36 G
#> 37 C
#> 38 C
#> 39 C
#> 40 TG
#> 41 C
#> 42 C
#> 43 A
#> 44 A
#> 45 A
#> 46 C
#> 47 A
#> 48 T
#> 49 C
#> 50 T
#> 51 GGAAGGAAGGAAGGAAA
#> 52 C
#> 53 G
#> 54 GATTCCATTCGATGATTCCATTCA
#> 55 TTCCATTCGATGATTCCATTCAATTCCATTCGATGATGATTCCATTCGAG
#> 56 CCATTCGATGATTCCATTCAA
#> 57 TCCGCCGCCGCCGCGGCTTTTTGCCCCCCACCCCCGCCGCCGCGGCTTTTTACCCGCCGCGGCTTTTTGCCCCCCCGCCGCCGTGGTTTTTTCCCCCCATCTCACCTCCGCTTTTTGCCCGCCGCGGCTTTTTGCCCCCACCCCGCCTCGGCTTTTTGCCAGCCACGGCTTTTTGCCCCCCGCCACCGCGGCTTTTTGTCCC
#> 58 CGCCGCCGCCGCGGCTTTTTGCCCCCCACCCCCGCCGCCGCGGCTTTTTACCCGCCGCGGCTTTTTGCCCCCCCG
#> 59 GCCGCCGCCGCGGCTTTTTGCCCCCCACCCCCGCCGCCGCGGCTTTTTACCCGCCGCGGCTTTTTGCCCCCCCGCCGCCGTGGTTTTTTCCCCCCATCTCACCTCCGCTTTTTGCCCGCCGCGGCTTTTTGCCCCCACCCCGCCTCGGCTTTTTGCCAGCCACGGCTTTTTGCCCC
#> 60 T
#> 61 T
#> 62 A
#> 63 G
#> 64 A
#> 65 ACAGCCAGCCAGCCAAGCCAGCCAAGCCAGCCAGGAAAGCCAGCCTGCCAAGCCAGCCAAGCCAGCCAGCCACTCAAGCCAGCCAAGTCAGCGAGCCAACCAAGCCAGCCAACTCAGCCAGCCACCTAAGCCAGCCAAGCCAGCCAGCCAGCCAAGCAAGCCAGCCAGCCAAGCCAGCCAAGCCAGCCAAGCCAGGCAGCCAGCCAAGCCAGCCAAGCCAGCCAGCCAGCCAAGCCAGCCAGCCAGCCCACACAGCCAAGC
#> 66 TCAAGCCAGCCAAGTCAGCGAGCCAACCAAGCCAGCCAACTCAGCCAGCCACCTAAGCCAGCCAAGCCAGCCAGCCAGCCAAGCAAGCCAGCCAGCCAAGCCAGCCAAGCCAGCCAAGCCAGGCAGCCAGC
#> 67 ACAGCCAAGACAGCCAGCCAGCCACGCAAGCCAAGCCAGCCAGCCAGGCAAGCCAGGCATGCCAGCCAAGCCATCCAGCCAGCCAAGCCAGGCGGCCAGCCAAGCCAGCCAAGCCACCCGGCCAGCCAAGCCACCCAAGCCACCCGGCCAGCCAGGCATCCAAGCCAGCCAAGT
#> 68 CAAGCCAGCCAGCTAGCCAAGCCACCCAGCCAGCCAGCCAGCCAAACCAGCCAAGCCAGCCAGCCAGCCAGCCAAGCCAGCCAAGCAAGCCAGCCAGCCAGCCAAGCCACGCAAGCCAGCCAGCCAGCCATGCCAGCCA
#> 69 CAAAAAAAAAAAAAA
#> 70 TCA
#> 71 TCTCTCC
#> 72 CTCTCCCTCTCTCTCTCTCTCTCTCCCT
#> 73 TCTCCCTCTCTCTCTCTCTCTCTCC
#> 74 CTCCCTCTCTCTCTCTCTCTCTCCCT
#> 75 G
#> 76 G
#> 77 C
#> 78 C
#> 79 GAAAAAAA
#> 80 AG
#> 81 C
#> 82 CTT
#> 83 CTTT
#> 84 TACACACAC
#> 85 TACACACAC
#> 86 TACACACAC
#> 87 TACACACAC
#> 88 TACACACAC
#> 89 C
#> 90 C
#> 91 TAA
#> 92 TAA
#> 93 G
#> 94 AT
#> 95 AAAAC
#> 96 AAAC
#> 97 A
#> 98 C
#> 99 C
#> 100 G
#> 101 GT
#> 102 G
#> 103 C
#> 104 T
#> 105 TACACAC
#> 106 C
#> 107 T
#> 108 A
#> 109 GGTGT
#> 110 GGTGT
#> 111 GGTGT
#> 112 GGTGT
#> 113 G
#> 114 G
#> 115 C
#> 116 G
#> 117 TCCAGTAAGAATCCAGTTCTC
#> 118 TCA
#> 119 C
#> 120 GAAAAA
#> 121 GAAAAA
#> 122 G
#> 123 ATTTATT
#> 124 ATT
#> 125 T
#> 126 T
#> 127 CA
#> 128 CA
#> 129 CT
#> 130 A
#> 131 AT
#> 132 ATTTT
#> 133 G
#> 134 CTT
#> 135 A
#> 136 TCAAGACATCCTCCACAGAGGACC
#> 137 CAA
#> 138 CAA
#> 139 CTTT
#> 140 CTTT
#> 141 T
#> 142 C
#> 143 AGTTATGGAGGTTAGGGAGGTTAGGGAAGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTAGGGAG
#> 144 TTATGGAGGTTAGGGAGGTTAG
#> 145 TGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTAG
#> 146 GGAGGTTAGGGAGGTTAGGGAGGTTAT
#> 147 AGGTT
#> 148 GTTA
#> 149 TTAGG
#> 150 AGGGAGGTTAGGGAG
#> 151 G
#> 152 G
#> 153 TAA
#> 154 TAA
#> 155 ATTTTTTTTT
#> 156 ATTTTTTTTT
#> 157 ATTTTTTTTT
#> 158 C
#> 159 G
#> 160 A
#> 161 A
#> 162 ACCCACACACACC
#> 163 C
#> 164 TA
#> 165 G
#> 166 A
#> 167 A
#> 168 CA
#> 169 A
#> 170 T
#> 171 T
#> 172 C
#> 173 GTATACATAAGATATATTATATATAATATATTATATAAATGTATTATATATAACATATTATATATAATATATT
#> 174 T
#> 175 T
#> z study
#> 1 0.669897348 gwas1
#> 2 -2.933840146 gwas1
#> 3 -1.461087314 gwas1
#> 4 1.380249919 gwas1
#> 5 0.919024233 gwas1
#> 6 -1.120649183 gwas1
#> 7 1.592203335 gwas1
#> 8 0.341351535 gwas1
#> 9 -0.197422053 gwas1
#> 10 -2.450772511 gwas1
#> 11 0.703656439 gwas1
#> 12 1.491149983 gwas1
#> 13 -0.799902659 gwas1
#> 14 0.701707417 gwas1
#> 15 -1.154482579 gwas1
#> 16 -0.885757448 gwas1
#> 17 -2.356886120 gwas1
#> 18 1.504130555 gwas1
#> 19 -0.642606099 gwas1
#> 20 -0.148436586 gwas1
#> 21 -0.369669557 gwas1
#> 22 2.060093786 gwas1
#> 23 -1.365424594 gwas1
#> 24 -0.879863066 gwas1
#> 25 1.302031888 gwas1
#> 26 -0.940937683 gwas1
#> 27 0.487766437 gwas1
#> 28 -0.768355209 gwas1
#> 29 0.475296689 gwas1
#> 30 -0.736066147 gwas1
#> 31 -0.962992675 gwas1
#> 32 0.099933461 gwas1
#> 33 2.554708301 gwas1
#> 34 -0.390380768 gwas1
#> 35 0.480652000 gwas1
#> 36 1.328106597 gwas1
#> 37 -2.498801748 gwas1
#> 38 -0.353758398 gwas1
#> 39 -0.891881582 gwas1
#> 40 3.017911741 gwas1
#> 41 0.470594294 gwas1
#> 42 -0.959004494 gwas1
#> 43 0.754848901 gwas1
#> 44 -1.855905901 gwas1
#> 45 0.864983545 gwas1
#> 46 -0.368226737 gwas1
#> 47 0.925424807 gwas1
#> 48 0.826528152 gwas1
#> 49 -0.746489583 gwas1
#> 50 -0.443852792 gwas1
#> 51 0.622144483 gwas1
#> 52 2.140633275 gwas1
#> 53 1.672167723 gwas1
#> 54 0.450538420 gwas1
#> 55 -0.922381817 gwas1
#> 56 0.970297129 gwas1
#> 57 0.314798746 gwas1
#> 58 -1.107864073 gwas1
#> 59 -0.960195073 gwas1
#> 60 -0.760341925 gwas1
#> 61 0.724376860 gwas1
#> 62 -0.006873117 gwas1
#> 63 0.881847048 gwas1
#> 64 3.062602156 gwas1
#> 65 0.343962121 gwas1
#> 66 -1.712041364 gwas1
#> 67 0.803583107 gwas1
#> 68 -0.574844760 gwas1
#> 69 -0.498219437 gwas1
#> 70 4.131720803 gwas1
#> 71 -0.222876318 gwas1
#> 72 0.381879731 gwas1
#> 73 1.049286103 gwas1
#> 74 0.555251420 gwas1
#> 75 -1.545294462 gwas1
#> 76 0.447633421 gwas1
#> 77 -0.756971150 gwas1
#> 78 -2.230811748 gwas1
#> 79 -0.725056455 gwas1
#> 80 -0.024204349 gwas1
#> 81 0.471999922 gwas1
#> 82 -2.737633939 gwas1
#> 83 -0.365189998 gwas1
#> 84 -0.779549150 gwas1
#> 85 2.288184108 gwas1
#> 86 2.562341769 gwas1
#> 87 1.342007543 gwas1
#> 88 0.466882112 gwas1
#> 89 0.003271000 gwas1
#> 90 -0.225474759 gwas1
#> 91 -1.537687049 gwas1
#> 92 -2.248287061 gwas1
#> 93 1.074911790 gwas1
#> 94 3.107043981 gwas1
#> 95 0.280600944 gwas1
#> 96 -0.759671951 gwas1
#> 97 1.085673279 gwas1
#> 98 0.521613583 gwas1
#> 99 0.684947689 gwas1
#> 100 -1.260535702 gwas1
#> 101 0.143854906 gwas1
#> 102 -0.481471483 gwas1
#> 103 -1.932355374 gwas1
#> 104 -2.023208819 gwas1
#> 105 -2.164319369 gwas1
#> 106 -0.995977717 gwas1
#> 107 1.366754672 gwas1
#> 108 -0.864920932 gwas1
#> 109 -0.202001942 gwas1
#> 110 -0.674890563 gwas1
#> 111 -0.416038223 gwas1
#> 112 -0.624174109 gwas1
#> 113 -0.027015339 gwas1
#> 114 -0.535601768 gwas1
#> 115 -0.135411084 gwas1
#> 116 -0.379613534 gwas1
#> 117 -0.369349174 gwas1
#> 118 -0.356709741 gwas1
#> 119 1.839641160 gwas1
#> 120 -0.472479028 gwas1
#> 121 1.459281515 gwas1
#> 122 6.789288191 gwas1
#> 123 0.043790821 gwas1
#> 124 0.969675074 gwas1
#> 125 -1.884907755 gwas1
#> 126 -1.212161942 gwas1
#> 127 4.020978730 gwas1
#> 128 -2.260093565 gwas1
#> 129 1.199758325 gwas1
#> 130 -0.708022102 gwas1
#> 131 2.571985029 gwas1
#> 132 1.022171031 gwas1
#> 133 0.839967121 gwas1
#> 134 -0.173360563 gwas1
#> 135 -1.873758505 gwas1
#> 136 -2.676356303 gwas1
#> 137 3.292765803 gwas1
#> 138 -0.667248777 gwas1
#> 139 0.132170273 gwas1
#> 140 -2.805484334 gwas1
#> 141 -0.771035998 gwas1
#> 142 1.736401755 gwas1
#> 143 0.015668485 gwas1
#> 144 0.366082733 gwas1
#> 145 0.287701865 gwas1
#> 146 -0.761724577 gwas1
#> 147 -1.554413489 gwas1
#> 148 -0.294052435 gwas1
#> 149 0.431650231 gwas1
#> 150 -1.477727803 gwas1
#> 151 2.062125671 gwas1
#> 152 -1.099305382 gwas1
#> 153 0.495291129 gwas1
#> 154 1.242328888 gwas1
#> 155 1.255709137 gwas1
#> 156 0.121123862 gwas1
#> 157 -0.068983875 gwas1
#> 158 -0.427370355 gwas1
#> 159 -0.516884295 gwas1
#> 160 -2.664396295 gwas1
#> 161 -0.324681850 gwas1
#> 162 1.145269644 gwas1
#> 163 1.382946720 gwas1
#> 164 3.268483767 gwas1
#> 165 2.826239506 gwas1
#> 166 -1.805260705 gwas1
#> 167 1.467859008 gwas1
#> 168 -0.794067434 gwas1
#> 169 -1.124449470 gwas1
#> 170 3.398057020 gwas1
#> 171 -1.274528490 gwas1
#> 172 0.325268398 gwas1
#> 173 0.843093142 gwas1
#> 174 -1.469343859 gwas1
#> 175 0.419229791 gwas1
#>
#> $weights
#> $weights$`chr22_1|protocol_example|bulk_rnaseq|ENSG00000130538|susie`
#> $weights$`chr22_1|protocol_example|bulk_rnaseq|ENSG00000130538|susie`$wgt
#> wgt
#> chr22:10685239:C:T 0.21977562
#> chr22:10761227:G:A 0.04982515
#> chr22:11285239:C:T -0.21149253
#> chr22:11601805:G:A 0.12291149
#> chr22:11791698:G:T -0.04959154
#> chr22:11797697:C:T -0.12839536
#> chr22:12194389:G:A -0.34592750
#> chr22:12207043:C:T 0.06026724
#> chr22:12350816:G:A -0.23130292
#> chr22:12352464:C:A 0.08731237
#> chr22:12370627:C:T 0.13038245
#> chr22:12571373:AGAAAGAAAGAAAGAAAGAAG:* -0.12153569
#> chr22:12571377:AGAAAGAAAGAAAGAAG:* -0.10692796
#> chr22:12571385:AGAAAGAAG:* -0.04899851
#> chr22:12571386:GAAAGAAGGA:* -0.04899851
#> chr22:12571389:AGAAGGAAAGAAGGAAAGAAAGGAAGAAGGAAAGAAG:* -0.04899851
#> chr22:12576050:T:A 0.13001826
#> chr22:12640661:G:T 0.18449970
#>
#> $weights$`chr22_1|protocol_example|bulk_rnaseq|ENSG00000130538|susie`$wgt_var
#> [1] 0.4937737
#>
#> $weights$`chr22_1|protocol_example|bulk_rnaseq|ENSG00000130538|susie`$type
#> [1] "bulk_rnaseq"
#>
#> $weights$`chr22_1|protocol_example|bulk_rnaseq|ENSG00000130538|susie`$context
#> [1] "bulk_rnaseq"
#>
#> $weights$`chr22_1|protocol_example|bulk_rnaseq|ENSG00000130538|susie`$gene_name
#> [1] "ENSG00000130538"
#>
#> $weights$`chr22_1|protocol_example|bulk_rnaseq|ENSG00000130538|susie`$study
#> [1] "protocol_example"
#>
#> $weights$`chr22_1|protocol_example|bulk_rnaseq|ENSG00000130538|susie`$method
#> [1] "susie"
#>
#> $weights$`chr22_1|protocol_example|bulk_rnaseq|ENSG00000130538|susie`$n_wgt
#> [1] 18
#>
#> $weights$`chr22_1|protocol_example|bulk_rnaseq|ENSG00000130538|susie`$chrom
#> [1] 22
#>
#> $weights$`chr22_1|protocol_example|bulk_rnaseq|ENSG00000130538|susie`$p0
#> [1] 10685239
#>
#> $weights$`chr22_1|protocol_example|bulk_rnaseq|ENSG00000130538|susie`$p1
#> [1] 18850784
#>
#> $weights$`chr22_1|protocol_example|bulk_rnaseq|ENSG00000130538|susie`$molecular_id
#> [1] "ENSG00000130538"
#>
#> $weights$`chr22_1|protocol_example|bulk_rnaseq|ENSG00000130538|susie`$weight_name
#> [1] "bulk_rnaseq_bulk_rnaseq"
#>
#> $weights$`chr22_1|protocol_example|bulk_rnaseq|ENSG00000130538|susie`$trait_pos
#> GRanges object with 1 range and 0 metadata columns:
#> seqnames ranges strand
#> <Rle> <IRanges> <Rle>
#> [1] chr22 10685239-18850784 *
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
#>
#>
#>
#> $snp_map
#> $snp_map$chr22_1
#> chrom id pos alt
#> 1 22 chr22:10685239:C:T 10685239 T
#> 2 22 chr22:10761227:G:A 10761227 A
#> 3 22 chr22:11285239:C:T 11285239 T
#> 4 22 chr22:11601805:G:A 11601805 A
#> 5 22 chr22:11791698:G:T 11791698 T
#> 6 22 chr22:11797697:C:T 11797697 T
#> 7 22 chr22:12044872:A:C 12044872 C
#> 8 22 chr22:12194389:G:A 12194389 A
#> 9 22 chr22:12207043:C:T 12207043 T
#> 10 22 chr22:12350816:G:A 12350816 A
#> 11 22 chr22:12352464:C:A 12352464 A
#> 12 22 chr22:12370627:C:T 12370627 T
#> 13 22 chr22:12383838:G:A 12383838 A
#> 14 22 chr22:12571373:AGAAAGAAAGAAAGAAAGAAG:* 12571373 *
#> 15 22 chr22:12571377:AGAAAGAAAGAAAGAAG:* 12571377 *
#> 16 22 chr22:12571385:AGAAAGAAG:* 12571385 *
#> 17 22 chr22:12571386:GAAAGAAGGA:* 12571386 *
#> 18 22 chr22:12571389:AGAAGGAAAGAAGGAAAGAAAGGAAGAAGGAAAGAAG:* 12571389 *
#> 19 22 chr22:12576050:T:A 12576050 A
#> 20 22 chr22:12640661:G:T 12640661 T
#> ref
#> 1 C
#> 2 G
#> 3 C
#> 4 G
#> 5 G
#> 6 C
#> 7 A
#> 8 G
#> 9 C
#> 10 G
#> 11 C
#> 12 C
#> 13 G
#> 14 AGAAAGAAAGAAAGAAAGAAG
#> 15 AGAAAGAAAGAAAGAAG
#> 16 AGAAAGAAG
#> 17 GAAAGAAGGA
#> 18 AGAAGGAAAGAAGGAAAGAAAGGAAGAAGGAAAGAAG
#> 19 T
#> 20 G
#>
#> $snp_map$chr22_2
#> chrom
#> 1 22
#> 2 22
#> 3 22
#> 4 22
#> 5 22
#> 6 22
#> 7 22
#> 8 22
#> 9 22
#> 10 22
#> 11 22
#> 12 22
#> 13 22
#> 14 22
#> 15 22
#> 16 22
#> 17 22
#> 18 22
#> 19 22
#> 20 22
#> 21 22
#> 22 22
#> 23 22
#> 24 22
#> 25 22
#> 26 22
#> 27 22
#> 28 22
#> 29 22
#> 30 22
#> 31 22
#> 32 22
#> 33 22
#> 34 22
#> 35 22
#> 36 22
#> 37 22
#> 38 22
#> 39 22
#> 40 22
#> 41 22
#> 42 22
#> 43 22
#> 44 22
#> 45 22
#> 46 22
#> 47 22
#> 48 22
#> 49 22
#> 50 22
#> 51 22
#> 52 22
#> 53 22
#> 54 22
#> 55 22
#> 56 22
#> 57 22
#> 58 22
#> 59 22
#> 60 22
#> 61 22
#> 62 22
#> 63 22
#> 64 22
#> 65 22
#> 66 22
#> 67 22
#> 68 22
#> 69 22
#> 70 22
#> 71 22
#> 72 22
#> 73 22
#> 74 22
#> 75 22
#> 76 22
#> 77 22
#> 78 22
#> 79 22
#> 80 22
#> 81 22
#> 82 22
#> 83 22
#> 84 22
#> 85 22
#> 86 22
#> 87 22
#> 88 22
#> 89 22
#> 90 22
#> 91 22
#> 92 22
#> 93 22
#> 94 22
#> 95 22
#> 96 22
#> 97 22
#> 98 22
#> 99 22
#> 100 22
#> 101 22
#> 102 22
#> 103 22
#> 104 22
#> 105 22
#> 106 22
#> 107 22
#> 108 22
#> 109 22
#> 110 22
#> 111 22
#> 112 22
#> 113 22
#> 114 22
#> 115 22
#> 116 22
#> 117 22
#> 118 22
#> 119 22
#> 120 22
#> 121 22
#> 122 22
#> 123 22
#> 124 22
#> 125 22
#> 126 22
#> 127 22
#> 128 22
#> 129 22
#> 130 22
#> 131 22
#> 132 22
#> 133 22
#> 134 22
#> 135 22
#> 136 22
#> 137 22
#> 138 22
#> 139 22
#> 140 22
#> 141 22
#> 142 22
#> 143 22
#> 144 22
#> 145 22
#> 146 22
#> 147 22
#> 148 22
#> 149 22
#> 150 22
#> 151 22
#> 152 22
#> 153 22
#> 154 22
#> 155 22
#> id
#> 1 chr22:15574750:C:A
#> 2 chr22:15635104:C:A
#> 3 chr22:15689224:A:C
#> 4 chr22:15773180:G:A
#> 5 chr22:15837995:CTTTCTTTCTTTCTTTTTCTTT:CTTTTTCTTTCTTTCTTTTTCTTT
#> 6 chr22:15838001:TTCTTTCTTTTTCTTTC:TTTTCTTTTTCTTTC
#> 7 chr22:15838002:TCTTTCTTTTTCTTTCTTC:*
#> 8 chr22:15838003:CTTTCTTTTTCTTT:ATTTCTTTTTCTTT
#> 9 chr22:15838003:CTTTCTTTTTCTTT:CTTTTTCTTTTTCTTT
#> 10 chr22:15838010:TTTCTTTCTTCCTTCCTTCCTTCCTTCCTTCCTCCCTTCCTTC:TCTTCTTTCTTCCTTCCTTCCTTCCTTCCTTCCTCCCTTCCTTC
#> 11 chr22:15839920:G:A
#> 12 chr22:15919156:A:T
#> 13 chr22:15927084:C:T
#> 14 chr22:15947643:T:C
#> 15 chr22:15984722:T:C
#> 16 chr22:16073625:G:T
#> 17 chr22:16102937:C:T
#> 18 chr22:16111042:C:CA
#> 19 chr22:16112049:C:A
#> 20 chr22:16112091:TG:CG
#> 21 chr22:16115854:C:T
#> 22 chr22:16124912:C:T
#> 23 chr22:16132992:A:G
#> 24 chr22:16187126:A:G
#> 25 chr22:16207293:A:G
#> 26 chr22:16214693:C:A
#> 27 chr22:16217062:A:G
#> 28 chr22:16224528:T:C
#> 29 chr22:16234309:C:T
#> 30 chr22:16244919:T:C
#> 31 chr22:16254612:GGAAGGAAGGAAGGAAA:AGAAGGAAGGAAGGAAA
#> 32 chr22:16258960:C:A
#> 33 chr22:16262035:G:A
#> 34 chr22:16262334:GATTCCATTCGATGATTCCATTCA:G
#> 35 chr22:16262336:TTCCATTCGATGATTCCATTCAATTCCATTCGATGATGATTCCATTCGAG:*
#> 36 chr22:16262338:CCATTCGATGATTCCATTCAA:*
#> 37 chr22:16386749:TCCGCCGCCGCCGCGGCTTTTTGCCCCCCACCCCCGCCGCCGCGGCTTTTTACCCGCCGCGGCTTTTTGCCCCCCCGCCGCCGTGGTTTTTTCCCCCCATCTCACCTCCGCTTTTTGCCCGCCGCGGCTTTTTGCCCCCACCCCGCCTCGGCTTTTTGCCAGCCACGGCTTTTTGCCCCCCGCCACCGCGGCTTTTTGTCCC:*
#> 38 chr22:16386751:CGCCGCCGCCGCGGCTTTTTGCCCCCCACCCCCGCCGCCGCGGCTTTTTACCCGCCGCGGCTTTTTGCCCCCCCG:*
#> 39 chr22:16386752:GCCGCCGCCGCGGCTTTTTGCCCCCCACCCCCGCCGCCGCGGCTTTTTACCCGCCGCGGCTTTTTGCCCCCCCGCCGCCGTGGTTTTTTCCCCCCATCTCACCTCCGCTTTTTGCCCGCCGCGGCTTTTTGCCCCCACCCCGCCTCGGCTTTTTGCCAGCCACGGCTTTTTGCCCC:CCCGCCGCCGCGGCTTTTTGCCCCCCACCCCCGCCGCCGCGGCTTTTTACCCGCCGCGGCTTTTTGCCCCCCCGCCGCCGTGGTTTTTTCCCCCCATCTCACCTCCGCTTTTTGCCCGCCGCGGCTTTTTGCCCCCACCCCGCCTCGGCTTTTTGCCAGCCACGGCTTTTTGCCCC
#> 40 chr22:16400343:T:C
#> 41 chr22:16427771:T:C
#> 42 chr22:16439458:A:G
#> 43 chr22:16442170:G:A
#> 44 chr22:16549730:A:G
#> 45 chr22:16560460:ACAGCCAGCCAGCCAAGCCAGCCAAGCCAGCCAGGAAAGCCAGCCTGCCAAGCCAGCCAAGCCAGCCAGCCACTCAAGCCAGCCAAGTCAGCGAGCCAACCAAGCCAGCCAACTCAGCCAGCCACCTAAGCCAGCCAAGCCAGCCAGCCAGCCAAGCAAGCCAGCCAGCCAAGCCAGCCAAGCCAGCCAAGCCAGGCAGCCAGCCAAGCCAGCCAAGCCAGCCAGCCAGCCAAGCCAGCCAGCCAGCCCACACAGCCAAGC:*
#> 46 chr22:16560533:TCAAGCCAGCCAAGTCAGCGAGCCAACCAAGCCAGCCAACTCAGCCAGCCACCTAAGCCAGCCAAGCCAGCCAGCCAGCCAAGCAAGCCAGCCAGCCAAGCCAGCCAAGCCAGCCAAGCCAGGCAGCCAGC:CCAAGCCAGCCAAGTCAGCGAGCCAACCAAGCCAGCCAACTCAGCCAGCCACCTAAGCCAGCCAAGCCAGCCAGCCAGCCAAGCAAGCCAGCCAGCCAAGCCAGCCAAGCCAGCCAAGCCAGGCAGCCAGC
#> 47 chr22:16566547:ACAGCCAAGACAGCCAGCCAGCCACGCAAGCCAAGCCAGCCAGCCAGGCAAGCCAGGCATGCCAGCCAAGCCATCCAGCCAGCCAAGCCAGGCGGCCAGCCAAGCCAGCCAAGCCACCCGGCCAGCCAAGCCACCCAAGCCACCCGGCCAGCCAGGCATCCAAGCCAGCCAAGT:*
#> 48 chr22:16566742:CAAGCCAGCCAGCTAGCCAAGCCACCCAGCCAGCCAGCCAGCCAAACCAGCCAAGCCAGCCAGCCAGCCAGCCAAGCCAGCCAAGCAAGCCAGCCAGCCAGCCAAGCCACGCAAGCCAGCCAGCCAGCCATGCCAGCCA:TAAGCCAGCCAGCTAGCCAAGCCACCCAGCCAGCCAGCCAGCCAAACCAGCCAAGCCAGCCAGCCAGCCAGCCAAGCCAGCCAAGCAAGCCAGCCAGCCAGCCAAGCCACGCAAGCCAGCCAGCCAGCCATGCCAGCCA
#> 49 chr22:16841646:CAAAAAAAAAAAAAA:AAAAAAAAAAAAAAA
#> 50 chr22:16845585:TCA:TCACA
#> 51 chr22:16909478:TCTCTCC:*
#> 52 chr22:16909479:CTCTCCCTCTCTCTCTCTCTCTCTCCCT:CCCCTCTCTCTCTCTCTCTCTCCCT
#> 53 chr22:16909480:TCTCCCTCTCTCTCTCTCTCTCTCC:*
#> 54 chr22:16909481:CTCCCTCTCTCTCTCTCTCTCTCCCT:*
#> 55 chr22:16970638:G:A
#> 56 chr22:16973012:G:A
#> 57 chr22:17014255:C:T
#> 58 chr22:17051853:C:T
#> 59 chr22:17079499:GAAAAAAA:GAAAAAAAA
#> 60 chr22:17113082:AG:A
#> 61 chr22:17136539:C:T
#> 62 chr22:17154616:CTT:CTTT
#> 63 chr22:17154616:CTTT:CT
#> 64 chr22:17157085:TACACACAC:CACACACAC
#> 65 chr22:17157085:TACACACAC:T
#> 66 chr22:17157085:TACACACAC:TACACACACACACACAC
#> 67 chr22:17157085:TACACACAC:TACACACACACACACACACAC
#> 68 chr22:17157085:TACACACAC:TACACACACACACACACACACACAC
#> 69 chr22:17168884:C:T
#> 70 chr22:17172477:C:T
#> 71 chr22:17187665:TAA:TA
#> 72 chr22:17187665:TAA:TAAA
#> 73 chr22:17187977:G:GC
#> 74 chr22:17209889:AT:ATT
#> 75 chr22:17216769:AAAAC:ACAAAC
#> 76 chr22:17216770:AAAC:ACAAC
#> 77 chr22:17216771:A:AC
#> 78 chr22:17216771:C:A
#> 79 chr22:17216789:C:CACAT
#> 80 chr22:17216799:G:T
#> 81 chr22:17221295:GT:G
#> 82 chr22:17302680:G:A
#> 83 chr22:17303055:C:T
#> 84 chr22:17326841:T:C
#> 85 chr22:17327911:TACACAC:TACAC
#> 86 chr22:17331260:C:CT
#> 87 chr22:17350100:T:C
#> 88 chr22:17375405:A:G
#> 89 chr22:17379581:GGTGT:GGT
#> 90 chr22:17379581:GGTGT:GGTGTGT
#> 91 chr22:17379581:GGTGT:GGTGTGTGT
#> 92 chr22:17379581:GGTGT:GGTGTGTGTGT
#> 93 chr22:17427850:G:T
#> 94 chr22:17429117:G:A
#> 95 chr22:17449676:C:A
#> 96 chr22:17466675:G:T
#> 97 chr22:17469609:TCCAGTAAGAATCCAGTTCTC:TCAGTAAGAATCCAGTTCTC
#> 98 chr22:17469610:TCA:CCA
#> 99 chr22:17518422:C:T
#> 100 chr22:17523010:GAAAAA:AAAAAA
#> 101 chr22:17523010:GAAAAA:GA
#> 102 chr22:17577230:G:A
#> 103 chr22:17585626:ATTTATT:A
#> 104 chr22:17585630:ATT:*
#> 105 chr22:17658972:T:C
#> 106 chr22:17667743:T:A
#> 107 chr22:17683132:CA:C
#> 108 chr22:17683132:CA:CAAA
#> 109 chr22:17687818:CT:C
#> 110 chr22:17706998:A:G
#> 111 chr22:17721525:AT:ATTTTT
#> 112 chr22:17721525:ATTTT:AT
#> 113 chr22:17726847:G:A
#> 114 chr22:17734310:CTT:C
#> 115 chr22:17763207:A:G
#> 116 chr22:17765138:TCAAGACATCCTCCACAGAGGACC:T
#> 117 chr22:17768872:CAA:CA
#> 118 chr22:17768872:CAA:CAAA
#> 119 chr22:17839567:CTTT:CT
#> 120 chr22:17839567:CTTT:CTT
#> 121 chr22:17846396:T:TA
#> 122 chr22:17860245:C:A
#> 123 chr22:17876770:AGTTATGGAGGTTAGGGAGGTTAGGGAAGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTAGGGAG:GGTTATGGAGGTTAGGGAGGTTAGGGAAGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTAGGGAG
#> 124 chr22:17876799:TTATGGAGGTTAGGGAGGTTAG:*
#> 125 chr22:17876802:TGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTAG:*
#> 126 chr22:17876803:GGAGGTTAGGGAGGTTAGGGAGGTTAT:*
#> 127 chr22:17876805:AGGTT:*
#> 128 chr22:17876807:GTTA:*
#> 129 chr22:17876808:TTAGG:*
#> 130 chr22:17876810:AGGGAGGTTAGGGAG:*
#> 131 chr22:17879807:G:A
#> 132 chr22:17880174:G:A
#> 133 chr22:17898107:TAA:TA
#> 134 chr22:17898107:TAA:TAAA
#> 135 chr22:17929265:ATTTTTTTTT:ATTTTTT
#> 136 chr22:17929265:ATTTTTTTTT:ATTTTTTT
#> 137 chr22:17929265:ATTTTTTTTT:ATTTTTTTT
#> 138 chr22:17949102:C:T
#> 139 chr22:17955812:G:A
#> 140 chr22:17967486:A:ACACACACC
#> 141 chr22:17967486:A:ACACACC
#> 142 chr22:17967492:ACCCACACACACC:ACACACACACC
#> 143 chr22:17967494:C:*
#> 144 chr22:17977536:TA:TAA
#> 145 chr22:17998075:G:GTGAA
#> 146 chr22:18001877:A:C
#> 147 chr22:18064272:A:T
#> 148 chr22:18150441:CA:C
#> 149 chr22:18159414:A:G
#> 150 chr22:18160557:T:C
#> 151 chr22:18166484:T:TGA
#> 152 chr22:18173426:C:A
#> 153 chr22:18730960:GTATACATAAGATATATTATATATAATATATTATATAAATGTATTATATATAACATATTATATATAATATATT:*
#> 154 chr22:18731027:T:C
#> 155 chr22:18850784:T:G
#> pos
#> 1 15574750
#> 2 15635104
#> 3 15689224
#> 4 15773180
#> 5 15837995
#> 6 15838001
#> 7 15838002
#> 8 15838003
#> 9 15838003
#> 10 15838010
#> 11 15839920
#> 12 15919156
#> 13 15927084
#> 14 15947643
#> 15 15984722
#> 16 16073625
#> 17 16102937
#> 18 16111042
#> 19 16112049
#> 20 16112091
#> 21 16115854
#> 22 16124912
#> 23 16132992
#> 24 16187126
#> 25 16207293
#> 26 16214693
#> 27 16217062
#> 28 16224528
#> 29 16234309
#> 30 16244919
#> 31 16254612
#> 32 16258960
#> 33 16262035
#> 34 16262334
#> 35 16262336
#> 36 16262338
#> 37 16386749
#> 38 16386751
#> 39 16386752
#> 40 16400343
#> 41 16427771
#> 42 16439458
#> 43 16442170
#> 44 16549730
#> 45 16560460
#> 46 16560533
#> 47 16566547
#> 48 16566742
#> 49 16841646
#> 50 16845585
#> 51 16909478
#> 52 16909479
#> 53 16909480
#> 54 16909481
#> 55 16970638
#> 56 16973012
#> 57 17014255
#> 58 17051853
#> 59 17079499
#> 60 17113082
#> 61 17136539
#> 62 17154616
#> 63 17154616
#> 64 17157085
#> 65 17157085
#> 66 17157085
#> 67 17157085
#> 68 17157085
#> 69 17168884
#> 70 17172477
#> 71 17187665
#> 72 17187665
#> 73 17187977
#> 74 17209889
#> 75 17216769
#> 76 17216770
#> 77 17216771
#> 78 17216771
#> 79 17216789
#> 80 17216799
#> 81 17221295
#> 82 17302680
#> 83 17303055
#> 84 17326841
#> 85 17327911
#> 86 17331260
#> 87 17350100
#> 88 17375405
#> 89 17379581
#> 90 17379581
#> 91 17379581
#> 92 17379581
#> 93 17427850
#> 94 17429117
#> 95 17449676
#> 96 17466675
#> 97 17469609
#> 98 17469610
#> 99 17518422
#> 100 17523010
#> 101 17523010
#> 102 17577230
#> 103 17585626
#> 104 17585630
#> 105 17658972
#> 106 17667743
#> 107 17683132
#> 108 17683132
#> 109 17687818
#> 110 17706998
#> 111 17721525
#> 112 17721525
#> 113 17726847
#> 114 17734310
#> 115 17763207
#> 116 17765138
#> 117 17768872
#> 118 17768872
#> 119 17839567
#> 120 17839567
#> 121 17846396
#> 122 17860245
#> 123 17876770
#> 124 17876799
#> 125 17876802
#> 126 17876803
#> 127 17876805
#> 128 17876807
#> 129 17876808
#> 130 17876810
#> 131 17879807
#> 132 17880174
#> 133 17898107
#> 134 17898107
#> 135 17929265
#> 136 17929265
#> 137 17929265
#> 138 17949102
#> 139 17955812
#> 140 17967486
#> 141 17967486
#> 142 17967492
#> 143 17967494
#> 144 17977536
#> 145 17998075
#> 146 18001877
#> 147 18064272
#> 148 18150441
#> 149 18159414
#> 150 18160557
#> 151 18166484
#> 152 18173426
#> 153 18730960
#> 154 18731027
#> 155 18850784
#> alt
#> 1 A
#> 2 A
#> 3 C
#> 4 A
#> 5 CTTTTTCTTTCTTTCTTTTTCTTT
#> 6 TTTTCTTTTTCTTTC
#> 7 *
#> 8 ATTTCTTTTTCTTT
#> 9 CTTTTTCTTTTTCTTT
#> 10 TCTTCTTTCTTCCTTCCTTCCTTCCTTCCTTCCTCCCTTCCTTC
#> 11 A
#> 12 T
#> 13 T
#> 14 C
#> 15 C
#> 16 T
#> 17 T
#> 18 CA
#> 19 A
#> 20 CG
#> 21 T
#> 22 T
#> 23 G
#> 24 G
#> 25 G
#> 26 A
#> 27 G
#> 28 C
#> 29 T
#> 30 C
#> 31 AGAAGGAAGGAAGGAAA
#> 32 A
#> 33 A
#> 34 G
#> 35 *
#> 36 *
#> 37 *
#> 38 *
#> 39 CCCGCCGCCGCGGCTTTTTGCCCCCCACCCCCGCCGCCGCGGCTTTTTACCCGCCGCGGCTTTTTGCCCCCCCGCCGCCGTGGTTTTTTCCCCCCATCTCACCTCCGCTTTTTGCCCGCCGCGGCTTTTTGCCCCCACCCCGCCTCGGCTTTTTGCCAGCCACGGCTTTTTGCCCC
#> 40 C
#> 41 C
#> 42 G
#> 43 A
#> 44 G
#> 45 *
#> 46 CCAAGCCAGCCAAGTCAGCGAGCCAACCAAGCCAGCCAACTCAGCCAGCCACCTAAGCCAGCCAAGCCAGCCAGCCAGCCAAGCAAGCCAGCCAGCCAAGCCAGCCAAGCCAGCCAAGCCAGGCAGCCAGC
#> 47 *
#> 48 TAAGCCAGCCAGCTAGCCAAGCCACCCAGCCAGCCAGCCAGCCAAACCAGCCAAGCCAGCCAGCCAGCCAGCCAAGCCAGCCAAGCAAGCCAGCCAGCCAGCCAAGCCACGCAAGCCAGCCAGCCAGCCATGCCAGCCA
#> 49 AAAAAAAAAAAAAAA
#> 50 TCACA
#> 51 *
#> 52 CCCCTCTCTCTCTCTCTCTCTCCCT
#> 53 *
#> 54 *
#> 55 A
#> 56 A
#> 57 T
#> 58 T
#> 59 GAAAAAAAA
#> 60 A
#> 61 T
#> 62 CTTT
#> 63 CT
#> 64 CACACACAC
#> 65 T
#> 66 TACACACACACACACAC
#> 67 TACACACACACACACACACAC
#> 68 TACACACACACACACACACACACAC
#> 69 T
#> 70 T
#> 71 TA
#> 72 TAAA
#> 73 GC
#> 74 ATT
#> 75 ACAAAC
#> 76 ACAAC
#> 77 AC
#> 78 A
#> 79 CACAT
#> 80 T
#> 81 G
#> 82 A
#> 83 T
#> 84 C
#> 85 TACAC
#> 86 CT
#> 87 C
#> 88 G
#> 89 GGT
#> 90 GGTGTGT
#> 91 GGTGTGTGT
#> 92 GGTGTGTGTGT
#> 93 T
#> 94 A
#> 95 A
#> 96 T
#> 97 TCAGTAAGAATCCAGTTCTC
#> 98 CCA
#> 99 T
#> 100 AAAAAA
#> 101 GA
#> 102 A
#> 103 A
#> 104 *
#> 105 C
#> 106 A
#> 107 C
#> 108 CAAA
#> 109 C
#> 110 G
#> 111 ATTTTT
#> 112 AT
#> 113 A
#> 114 C
#> 115 G
#> 116 T
#> 117 CA
#> 118 CAAA
#> 119 CT
#> 120 CTT
#> 121 TA
#> 122 A
#> 123 GGTTATGGAGGTTAGGGAGGTTAGGGAAGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTAGGGAG
#> 124 *
#> 125 *
#> 126 *
#> 127 *
#> 128 *
#> 129 *
#> 130 *
#> 131 A
#> 132 A
#> 133 TA
#> 134 TAAA
#> 135 ATTTTTT
#> 136 ATTTTTTT
#> 137 ATTTTTTTT
#> 138 T
#> 139 A
#> 140 ACACACACC
#> 141 ACACACC
#> 142 ACACACACACC
#> 143 *
#> 144 TAA
#> 145 GTGAA
#> 146 C
#> 147 T
#> 148 C
#> 149 G
#> 150 C
#> 151 TGA
#> 152 A
#> 153 *
#> 154 C
#> 155 G
#> ref
#> 1 C
#> 2 C
#> 3 A
#> 4 G
#> 5 CTTTCTTTCTTTCTTTTTCTTT
#> 6 TTCTTTCTTTTTCTTTC
#> 7 TCTTTCTTTTTCTTTCTTC
#> 8 CTTTCTTTTTCTTT
#> 9 CTTTCTTTTTCTTT
#> 10 TTTCTTTCTTCCTTCCTTCCTTCCTTCCTTCCTCCCTTCCTTC
#> 11 G
#> 12 A
#> 13 C
#> 14 T
#> 15 T
#> 16 G
#> 17 C
#> 18 C
#> 19 C
#> 20 TG
#> 21 C
#> 22 C
#> 23 A
#> 24 A
#> 25 A
#> 26 C
#> 27 A
#> 28 T
#> 29 C
#> 30 T
#> 31 GGAAGGAAGGAAGGAAA
#> 32 C
#> 33 G
#> 34 GATTCCATTCGATGATTCCATTCA
#> 35 TTCCATTCGATGATTCCATTCAATTCCATTCGATGATGATTCCATTCGAG
#> 36 CCATTCGATGATTCCATTCAA
#> 37 TCCGCCGCCGCCGCGGCTTTTTGCCCCCCACCCCCGCCGCCGCGGCTTTTTACCCGCCGCGGCTTTTTGCCCCCCCGCCGCCGTGGTTTTTTCCCCCCATCTCACCTCCGCTTTTTGCCCGCCGCGGCTTTTTGCCCCCACCCCGCCTCGGCTTTTTGCCAGCCACGGCTTTTTGCCCCCCGCCACCGCGGCTTTTTGTCCC
#> 38 CGCCGCCGCCGCGGCTTTTTGCCCCCCACCCCCGCCGCCGCGGCTTTTTACCCGCCGCGGCTTTTTGCCCCCCCG
#> 39 GCCGCCGCCGCGGCTTTTTGCCCCCCACCCCCGCCGCCGCGGCTTTTTACCCGCCGCGGCTTTTTGCCCCCCCGCCGCCGTGGTTTTTTCCCCCCATCTCACCTCCGCTTTTTGCCCGCCGCGGCTTTTTGCCCCCACCCCGCCTCGGCTTTTTGCCAGCCACGGCTTTTTGCCCC
#> 40 T
#> 41 T
#> 42 A
#> 43 G
#> 44 A
#> 45 ACAGCCAGCCAGCCAAGCCAGCCAAGCCAGCCAGGAAAGCCAGCCTGCCAAGCCAGCCAAGCCAGCCAGCCACTCAAGCCAGCCAAGTCAGCGAGCCAACCAAGCCAGCCAACTCAGCCAGCCACCTAAGCCAGCCAAGCCAGCCAGCCAGCCAAGCAAGCCAGCCAGCCAAGCCAGCCAAGCCAGCCAAGCCAGGCAGCCAGCCAAGCCAGCCAAGCCAGCCAGCCAGCCAAGCCAGCCAGCCAGCCCACACAGCCAAGC
#> 46 TCAAGCCAGCCAAGTCAGCGAGCCAACCAAGCCAGCCAACTCAGCCAGCCACCTAAGCCAGCCAAGCCAGCCAGCCAGCCAAGCAAGCCAGCCAGCCAAGCCAGCCAAGCCAGCCAAGCCAGGCAGCCAGC
#> 47 ACAGCCAAGACAGCCAGCCAGCCACGCAAGCCAAGCCAGCCAGCCAGGCAAGCCAGGCATGCCAGCCAAGCCATCCAGCCAGCCAAGCCAGGCGGCCAGCCAAGCCAGCCAAGCCACCCGGCCAGCCAAGCCACCCAAGCCACCCGGCCAGCCAGGCATCCAAGCCAGCCAAGT
#> 48 CAAGCCAGCCAGCTAGCCAAGCCACCCAGCCAGCCAGCCAGCCAAACCAGCCAAGCCAGCCAGCCAGCCAGCCAAGCCAGCCAAGCAAGCCAGCCAGCCAGCCAAGCCACGCAAGCCAGCCAGCCAGCCATGCCAGCCA
#> 49 CAAAAAAAAAAAAAA
#> 50 TCA
#> 51 TCTCTCC
#> 52 CTCTCCCTCTCTCTCTCTCTCTCTCCCT
#> 53 TCTCCCTCTCTCTCTCTCTCTCTCC
#> 54 CTCCCTCTCTCTCTCTCTCTCTCCCT
#> 55 G
#> 56 G
#> 57 C
#> 58 C
#> 59 GAAAAAAA
#> 60 AG
#> 61 C
#> 62 CTT
#> 63 CTTT
#> 64 TACACACAC
#> 65 TACACACAC
#> 66 TACACACAC
#> 67 TACACACAC
#> 68 TACACACAC
#> 69 C
#> 70 C
#> 71 TAA
#> 72 TAA
#> 73 G
#> 74 AT
#> 75 AAAAC
#> 76 AAAC
#> 77 A
#> 78 C
#> 79 C
#> 80 G
#> 81 GT
#> 82 G
#> 83 C
#> 84 T
#> 85 TACACAC
#> 86 C
#> 87 T
#> 88 A
#> 89 GGTGT
#> 90 GGTGT
#> 91 GGTGT
#> 92 GGTGT
#> 93 G
#> 94 G
#> 95 C
#> 96 G
#> 97 TCCAGTAAGAATCCAGTTCTC
#> 98 TCA
#> 99 C
#> 100 GAAAAA
#> 101 GAAAAA
#> 102 G
#> 103 ATTTATT
#> 104 ATT
#> 105 T
#> 106 T
#> 107 CA
#> 108 CA
#> 109 CT
#> 110 A
#> 111 AT
#> 112 ATTTT
#> 113 G
#> 114 CTT
#> 115 A
#> 116 TCAAGACATCCTCCACAGAGGACC
#> 117 CAA
#> 118 CAA
#> 119 CTTT
#> 120 CTTT
#> 121 T
#> 122 C
#> 123 AGTTATGGAGGTTAGGGAGGTTAGGGAAGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTAGGGAG
#> 124 TTATGGAGGTTAGGGAGGTTAG
#> 125 TGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTAG
#> 126 GGAGGTTAGGGAGGTTAGGGAGGTTAT
#> 127 AGGTT
#> 128 GTTA
#> 129 TTAGG
#> 130 AGGGAGGTTAGGGAG
#> 131 G
#> 132 G
#> 133 TAA
#> 134 TAA
#> 135 ATTTTTTTTT
#> 136 ATTTTTTTTT
#> 137 ATTTTTTTTT
#> 138 C
#> 139 G
#> 140 A
#> 141 A
#> 142 ACCCACACACACC
#> 143 C
#> 144 TA
#> 145 G
#> 146 A
#> 147 A
#> 148 CA
#> 149 A
#> 150 T
#> 151 T
#> 152 C
#> 153 GTATACATAAGATATATTATATATAATATATTATATAAATGTATTATATATAACATATTATATATAATATATT
#> 154 T
#> 155 T
#>
#>
#> $LD_map
#> region_id LD_file
#> 1 chr22_1 /tmp/RtmpmBLZhq/pecotmr-ctwas-ld/1_chr22_1.ld
#> 2 chr22_2 /tmp/RtmpmBLZhq/pecotmr-ctwas-ld/2_chr22_2.ld
#> SNP_file
#> 1 /tmp/RtmpmBLZhq/pecotmr-ctwas-ld/1_chr22_1.ld
#> 2 /tmp/RtmpmBLZhq/pecotmr-ctwas-ld/2_chr22_2.ld
#>
#> $LD_loader_fun
#> function (LD_file)
#> {
#> .ctwasPanelLd(.ctwasLoaderPanel(sys.function(), LD_file,
#> "LD loader"))
#> }
#> <bytecode: 0x559e986fe2e8>
#> <environment: namespace:pecotmr>
#> attr(,"ldPanelsByRegion")
#> attr(,"ldPanelsByRegion")$`/tmp/RtmpmBLZhq/pecotmr-ctwas-ld/1_chr22_1.ld`
#> attr(,"ldPanelsByRegion")$`/tmp/RtmpmBLZhq/pecotmr-ctwas-ld/1_chr22_1.ld`$snpInfo
#> chrom id pos alt
#> 1 22 chr22:10685239:C:T 10685239 T
#> 2 22 chr22:10761227:G:A 10761227 A
#> 3 22 chr22:11285239:C:T 11285239 T
#> 4 22 chr22:11601805:G:A 11601805 A
#> 5 22 chr22:11791698:G:T 11791698 T
#> 6 22 chr22:11797697:C:T 11797697 T
#> 7 22 chr22:12044872:A:C 12044872 C
#> 8 22 chr22:12194389:G:A 12194389 A
#> 9 22 chr22:12207043:C:T 12207043 T
#> 10 22 chr22:12350816:G:A 12350816 A
#> 11 22 chr22:12352464:C:A 12352464 A
#> 12 22 chr22:12370627:C:T 12370627 T
#> 13 22 chr22:12383838:G:A 12383838 A
#> 14 22 chr22:12571373:AGAAAGAAAGAAAGAAAGAAG:* 12571373 *
#> 15 22 chr22:12571377:AGAAAGAAAGAAAGAAG:* 12571377 *
#> 16 22 chr22:12571385:AGAAAGAAG:* 12571385 *
#> 17 22 chr22:12571386:GAAAGAAGGA:* 12571386 *
#> 18 22 chr22:12571389:AGAAGGAAAGAAGGAAAGAAAGGAAGAAGGAAAGAAG:* 12571389 *
#> 19 22 chr22:12576050:T:A 12576050 A
#> 20 22 chr22:12640661:G:T 12640661 T
#> ref
#> 1 C
#> 2 G
#> 3 C
#> 4 G
#> 5 G
#> 6 C
#> 7 A
#> 8 G
#> 9 C
#> 10 G
#> 11 C
#> 12 C
#> 13 G
#> 14 AGAAAGAAAGAAAGAAAGAAG
#> 15 AGAAAGAAAGAAAGAAG
#> 16 AGAAAGAAG
#> 17 GAAAGAAGGA
#> 18 AGAAGGAAAGAAGGAAAGAAAGGAAGAAGGAAAGAAG
#> 19 T
#> 20 G
#>
#> attr(,"ldPanelsByRegion")$`/tmp/RtmpmBLZhq/pecotmr-ctwas-ld/1_chr22_1.ld`$variance
#> chr22:10685239:C:T
#> 0.10986052
#> chr22:10761227:G:A
#> 0.25500000
#> chr22:11285239:C:T
#> 0.15277722
#> chr22:11601805:G:A
#> 0.10986052
#> chr22:11791698:G:T
#> 0.09500000
#> chr22:11797697:C:T
#> 0.09500000
#> chr22:12044872:A:C
#> 0.07986172
#> chr22:12194389:G:A
#> 0.10986052
#> chr22:12207043:C:T
#> 0.10986052
#> chr22:12350816:G:A
#> 0.10986052
#> chr22:12352464:C:A
#> 0.21875000
#> chr22:12370627:C:T
#> 0.21875000
#> chr22:12383838:G:A
#> 0.07986172
#> chr22:12571373:AGAAAGAAAGAAAGAAAGAAG:*
#> 0.20611162
#> chr22:12571377:AGAAAGAAAGAAAGAAG:*
#> 0.19319392
#> chr22:12571385:AGAAAGAAG:*
#> 0.16652832
#> chr22:12571386:GAAAGAAGGA:*
#> 0.16652832
#> chr22:12571389:AGAAGGAAAGAAGGAAAGAAAGGAAGAAGGAAAGAAG:*
#> 0.16652832
#> chr22:12576050:T:A
#> 0.21875000
#> chr22:12640661:G:T
#> 0.18000000
#>
#> attr(,"ldPanelsByRegion")$`/tmp/RtmpmBLZhq/pecotmr-ctwas-ld/1_chr22_1.ld`$sketch
#> class: RangedSummarizedExperiment
#> dim: 20 1000
#> metadata(2): genotypeSource ldProjection
#> assays(1): dosage
#> rownames(20): chr22:10685239:C:T chr22:10761227:G:A ...
#> chr22:12576050:T:A chr22:12640661:G:T
#> rowData names(4): SNP A1 A2 AF
#> colnames(1000): S1 S2 ... S999 S1000
#> colData names(0):
#>
#>
#> attr(,"ldPanelsByRegion")$`/tmp/RtmpmBLZhq/pecotmr-ctwas-ld/2_chr22_2.ld`
#> attr(,"ldPanelsByRegion")$`/tmp/RtmpmBLZhq/pecotmr-ctwas-ld/2_chr22_2.ld`$snpInfo
#> chrom
#> 1 22
#> 2 22
#> 3 22
#> 4 22
#> 5 22
#> 6 22
#> 7 22
#> 8 22
#> 9 22
#> 10 22
#> 11 22
#> 12 22
#> 13 22
#> 14 22
#> 15 22
#> 16 22
#> 17 22
#> 18 22
#> 19 22
#> 20 22
#> 21 22
#> 22 22
#> 23 22
#> 24 22
#> 25 22
#> 26 22
#> 27 22
#> 28 22
#> 29 22
#> 30 22
#> 31 22
#> 32 22
#> 33 22
#> 34 22
#> 35 22
#> 36 22
#> 37 22
#> 38 22
#> 39 22
#> 40 22
#> 41 22
#> 42 22
#> 43 22
#> 44 22
#> 45 22
#> 46 22
#> 47 22
#> 48 22
#> 49 22
#> 50 22
#> 51 22
#> 52 22
#> 53 22
#> 54 22
#> 55 22
#> 56 22
#> 57 22
#> 58 22
#> 59 22
#> 60 22
#> 61 22
#> 62 22
#> 63 22
#> 64 22
#> 65 22
#> 66 22
#> 67 22
#> 68 22
#> 69 22
#> 70 22
#> 71 22
#> 72 22
#> 73 22
#> 74 22
#> 75 22
#> 76 22
#> 77 22
#> 78 22
#> 79 22
#> 80 22
#> 81 22
#> 82 22
#> 83 22
#> 84 22
#> 85 22
#> 86 22
#> 87 22
#> 88 22
#> 89 22
#> 90 22
#> 91 22
#> 92 22
#> 93 22
#> 94 22
#> 95 22
#> 96 22
#> 97 22
#> 98 22
#> 99 22
#> 100 22
#> 101 22
#> 102 22
#> 103 22
#> 104 22
#> 105 22
#> 106 22
#> 107 22
#> 108 22
#> 109 22
#> 110 22
#> 111 22
#> 112 22
#> 113 22
#> 114 22
#> 115 22
#> 116 22
#> 117 22
#> 118 22
#> 119 22
#> 120 22
#> 121 22
#> 122 22
#> 123 22
#> 124 22
#> 125 22
#> 126 22
#> 127 22
#> 128 22
#> 129 22
#> 130 22
#> 131 22
#> 132 22
#> 133 22
#> 134 22
#> 135 22
#> 136 22
#> 137 22
#> 138 22
#> 139 22
#> 140 22
#> 141 22
#> 142 22
#> 143 22
#> 144 22
#> 145 22
#> 146 22
#> 147 22
#> 148 22
#> 149 22
#> 150 22
#> 151 22
#> 152 22
#> 153 22
#> 154 22
#> 155 22
#> id
#> 1 chr22:15574750:C:A
#> 2 chr22:15635104:C:A
#> 3 chr22:15689224:A:C
#> 4 chr22:15773180:G:A
#> 5 chr22:15837995:CTTTCTTTCTTTCTTTTTCTTT:CTTTTTCTTTCTTTCTTTTTCTTT
#> 6 chr22:15838001:TTCTTTCTTTTTCTTTC:TTTTCTTTTTCTTTC
#> 7 chr22:15838002:TCTTTCTTTTTCTTTCTTC:*
#> 8 chr22:15838003:CTTTCTTTTTCTTT:ATTTCTTTTTCTTT
#> 9 chr22:15838003:CTTTCTTTTTCTTT:CTTTTTCTTTTTCTTT
#> 10 chr22:15838010:TTTCTTTCTTCCTTCCTTCCTTCCTTCCTTCCTCCCTTCCTTC:TCTTCTTTCTTCCTTCCTTCCTTCCTTCCTTCCTCCCTTCCTTC
#> 11 chr22:15839920:G:A
#> 12 chr22:15919156:A:T
#> 13 chr22:15927084:C:T
#> 14 chr22:15947643:T:C
#> 15 chr22:15984722:T:C
#> 16 chr22:16073625:G:T
#> 17 chr22:16102937:C:T
#> 18 chr22:16111042:C:CA
#> 19 chr22:16112049:C:A
#> 20 chr22:16112091:TG:CG
#> 21 chr22:16115854:C:T
#> 22 chr22:16124912:C:T
#> 23 chr22:16132992:A:G
#> 24 chr22:16187126:A:G
#> 25 chr22:16207293:A:G
#> 26 chr22:16214693:C:A
#> 27 chr22:16217062:A:G
#> 28 chr22:16224528:T:C
#> 29 chr22:16234309:C:T
#> 30 chr22:16244919:T:C
#> 31 chr22:16254612:GGAAGGAAGGAAGGAAA:AGAAGGAAGGAAGGAAA
#> 32 chr22:16258960:C:A
#> 33 chr22:16262035:G:A
#> 34 chr22:16262334:GATTCCATTCGATGATTCCATTCA:G
#> 35 chr22:16262336:TTCCATTCGATGATTCCATTCAATTCCATTCGATGATGATTCCATTCGAG:*
#> 36 chr22:16262338:CCATTCGATGATTCCATTCAA:*
#> 37 chr22:16386749:TCCGCCGCCGCCGCGGCTTTTTGCCCCCCACCCCCGCCGCCGCGGCTTTTTACCCGCCGCGGCTTTTTGCCCCCCCGCCGCCGTGGTTTTTTCCCCCCATCTCACCTCCGCTTTTTGCCCGCCGCGGCTTTTTGCCCCCACCCCGCCTCGGCTTTTTGCCAGCCACGGCTTTTTGCCCCCCGCCACCGCGGCTTTTTGTCCC:*
#> 38 chr22:16386751:CGCCGCCGCCGCGGCTTTTTGCCCCCCACCCCCGCCGCCGCGGCTTTTTACCCGCCGCGGCTTTTTGCCCCCCCG:*
#> 39 chr22:16386752:GCCGCCGCCGCGGCTTTTTGCCCCCCACCCCCGCCGCCGCGGCTTTTTACCCGCCGCGGCTTTTTGCCCCCCCGCCGCCGTGGTTTTTTCCCCCCATCTCACCTCCGCTTTTTGCCCGCCGCGGCTTTTTGCCCCCACCCCGCCTCGGCTTTTTGCCAGCCACGGCTTTTTGCCCC:CCCGCCGCCGCGGCTTTTTGCCCCCCACCCCCGCCGCCGCGGCTTTTTACCCGCCGCGGCTTTTTGCCCCCCCGCCGCCGTGGTTTTTTCCCCCCATCTCACCTCCGCTTTTTGCCCGCCGCGGCTTTTTGCCCCCACCCCGCCTCGGCTTTTTGCCAGCCACGGCTTTTTGCCCC
#> 40 chr22:16400343:T:C
#> 41 chr22:16427771:T:C
#> 42 chr22:16439458:A:G
#> 43 chr22:16442170:G:A
#> 44 chr22:16549730:A:G
#> 45 chr22:16560460:ACAGCCAGCCAGCCAAGCCAGCCAAGCCAGCCAGGAAAGCCAGCCTGCCAAGCCAGCCAAGCCAGCCAGCCACTCAAGCCAGCCAAGTCAGCGAGCCAACCAAGCCAGCCAACTCAGCCAGCCACCTAAGCCAGCCAAGCCAGCCAGCCAGCCAAGCAAGCCAGCCAGCCAAGCCAGCCAAGCCAGCCAAGCCAGGCAGCCAGCCAAGCCAGCCAAGCCAGCCAGCCAGCCAAGCCAGCCAGCCAGCCCACACAGCCAAGC:*
#> 46 chr22:16560533:TCAAGCCAGCCAAGTCAGCGAGCCAACCAAGCCAGCCAACTCAGCCAGCCACCTAAGCCAGCCAAGCCAGCCAGCCAGCCAAGCAAGCCAGCCAGCCAAGCCAGCCAAGCCAGCCAAGCCAGGCAGCCAGC:CCAAGCCAGCCAAGTCAGCGAGCCAACCAAGCCAGCCAACTCAGCCAGCCACCTAAGCCAGCCAAGCCAGCCAGCCAGCCAAGCAAGCCAGCCAGCCAAGCCAGCCAAGCCAGCCAAGCCAGGCAGCCAGC
#> 47 chr22:16566547:ACAGCCAAGACAGCCAGCCAGCCACGCAAGCCAAGCCAGCCAGCCAGGCAAGCCAGGCATGCCAGCCAAGCCATCCAGCCAGCCAAGCCAGGCGGCCAGCCAAGCCAGCCAAGCCACCCGGCCAGCCAAGCCACCCAAGCCACCCGGCCAGCCAGGCATCCAAGCCAGCCAAGT:*
#> 48 chr22:16566742:CAAGCCAGCCAGCTAGCCAAGCCACCCAGCCAGCCAGCCAGCCAAACCAGCCAAGCCAGCCAGCCAGCCAGCCAAGCCAGCCAAGCAAGCCAGCCAGCCAGCCAAGCCACGCAAGCCAGCCAGCCAGCCATGCCAGCCA:TAAGCCAGCCAGCTAGCCAAGCCACCCAGCCAGCCAGCCAGCCAAACCAGCCAAGCCAGCCAGCCAGCCAGCCAAGCCAGCCAAGCAAGCCAGCCAGCCAGCCAAGCCACGCAAGCCAGCCAGCCAGCCATGCCAGCCA
#> 49 chr22:16841646:CAAAAAAAAAAAAAA:AAAAAAAAAAAAAAA
#> 50 chr22:16845585:TCA:TCACA
#> 51 chr22:16909478:TCTCTCC:*
#> 52 chr22:16909479:CTCTCCCTCTCTCTCTCTCTCTCTCCCT:CCCCTCTCTCTCTCTCTCTCTCCCT
#> 53 chr22:16909480:TCTCCCTCTCTCTCTCTCTCTCTCC:*
#> 54 chr22:16909481:CTCCCTCTCTCTCTCTCTCTCTCCCT:*
#> 55 chr22:16970638:G:A
#> 56 chr22:16973012:G:A
#> 57 chr22:17014255:C:T
#> 58 chr22:17051853:C:T
#> 59 chr22:17079499:GAAAAAAA:GAAAAAAAA
#> 60 chr22:17113082:AG:A
#> 61 chr22:17136539:C:T
#> 62 chr22:17154616:CTT:CTTT
#> 63 chr22:17154616:CTTT:CT
#> 64 chr22:17157085:TACACACAC:CACACACAC
#> 65 chr22:17157085:TACACACAC:T
#> 66 chr22:17157085:TACACACAC:TACACACACACACACAC
#> 67 chr22:17157085:TACACACAC:TACACACACACACACACACAC
#> 68 chr22:17157085:TACACACAC:TACACACACACACACACACACACAC
#> 69 chr22:17168884:C:T
#> 70 chr22:17172477:C:T
#> 71 chr22:17187665:TAA:TA
#> 72 chr22:17187665:TAA:TAAA
#> 73 chr22:17187977:G:GC
#> 74 chr22:17209889:AT:ATT
#> 75 chr22:17216769:AAAAC:ACAAAC
#> 76 chr22:17216770:AAAC:ACAAC
#> 77 chr22:17216771:A:AC
#> 78 chr22:17216771:C:A
#> 79 chr22:17216789:C:CACAT
#> 80 chr22:17216799:G:T
#> 81 chr22:17221295:GT:G
#> 82 chr22:17302680:G:A
#> 83 chr22:17303055:C:T
#> 84 chr22:17326841:T:C
#> 85 chr22:17327911:TACACAC:TACAC
#> 86 chr22:17331260:C:CT
#> 87 chr22:17350100:T:C
#> 88 chr22:17375405:A:G
#> 89 chr22:17379581:GGTGT:GGT
#> 90 chr22:17379581:GGTGT:GGTGTGT
#> 91 chr22:17379581:GGTGT:GGTGTGTGT
#> 92 chr22:17379581:GGTGT:GGTGTGTGTGT
#> 93 chr22:17427850:G:T
#> 94 chr22:17429117:G:A
#> 95 chr22:17449676:C:A
#> 96 chr22:17466675:G:T
#> 97 chr22:17469609:TCCAGTAAGAATCCAGTTCTC:TCAGTAAGAATCCAGTTCTC
#> 98 chr22:17469610:TCA:CCA
#> 99 chr22:17518422:C:T
#> 100 chr22:17523010:GAAAAA:AAAAAA
#> 101 chr22:17523010:GAAAAA:GA
#> 102 chr22:17577230:G:A
#> 103 chr22:17585626:ATTTATT:A
#> 104 chr22:17585630:ATT:*
#> 105 chr22:17658972:T:C
#> 106 chr22:17667743:T:A
#> 107 chr22:17683132:CA:C
#> 108 chr22:17683132:CA:CAAA
#> 109 chr22:17687818:CT:C
#> 110 chr22:17706998:A:G
#> 111 chr22:17721525:AT:ATTTTT
#> 112 chr22:17721525:ATTTT:AT
#> 113 chr22:17726847:G:A
#> 114 chr22:17734310:CTT:C
#> 115 chr22:17763207:A:G
#> 116 chr22:17765138:TCAAGACATCCTCCACAGAGGACC:T
#> 117 chr22:17768872:CAA:CA
#> 118 chr22:17768872:CAA:CAAA
#> 119 chr22:17839567:CTTT:CT
#> 120 chr22:17839567:CTTT:CTT
#> 121 chr22:17846396:T:TA
#> 122 chr22:17860245:C:A
#> 123 chr22:17876770:AGTTATGGAGGTTAGGGAGGTTAGGGAAGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTAGGGAG:GGTTATGGAGGTTAGGGAGGTTAGGGAAGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTAGGGAG
#> 124 chr22:17876799:TTATGGAGGTTAGGGAGGTTAG:*
#> 125 chr22:17876802:TGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTAG:*
#> 126 chr22:17876803:GGAGGTTAGGGAGGTTAGGGAGGTTAT:*
#> 127 chr22:17876805:AGGTT:*
#> 128 chr22:17876807:GTTA:*
#> 129 chr22:17876808:TTAGG:*
#> 130 chr22:17876810:AGGGAGGTTAGGGAG:*
#> 131 chr22:17879807:G:A
#> 132 chr22:17880174:G:A
#> 133 chr22:17898107:TAA:TA
#> 134 chr22:17898107:TAA:TAAA
#> 135 chr22:17929265:ATTTTTTTTT:ATTTTTT
#> 136 chr22:17929265:ATTTTTTTTT:ATTTTTTT
#> 137 chr22:17929265:ATTTTTTTTT:ATTTTTTTT
#> 138 chr22:17949102:C:T
#> 139 chr22:17955812:G:A
#> 140 chr22:17967486:A:ACACACACC
#> 141 chr22:17967486:A:ACACACC
#> 142 chr22:17967492:ACCCACACACACC:ACACACACACC
#> 143 chr22:17967494:C:*
#> 144 chr22:17977536:TA:TAA
#> 145 chr22:17998075:G:GTGAA
#> 146 chr22:18001877:A:C
#> 147 chr22:18064272:A:T
#> 148 chr22:18150441:CA:C
#> 149 chr22:18159414:A:G
#> 150 chr22:18160557:T:C
#> 151 chr22:18166484:T:TGA
#> 152 chr22:18173426:C:A
#> 153 chr22:18730960:GTATACATAAGATATATTATATATAATATATTATATAAATGTATTATATATAACATATTATATATAATATATT:*
#> 154 chr22:18731027:T:C
#> 155 chr22:18850784:T:G
#> pos
#> 1 15574750
#> 2 15635104
#> 3 15689224
#> 4 15773180
#> 5 15837995
#> 6 15838001
#> 7 15838002
#> 8 15838003
#> 9 15838003
#> 10 15838010
#> 11 15839920
#> 12 15919156
#> 13 15927084
#> 14 15947643
#> 15 15984722
#> 16 16073625
#> 17 16102937
#> 18 16111042
#> 19 16112049
#> 20 16112091
#> 21 16115854
#> 22 16124912
#> 23 16132992
#> 24 16187126
#> 25 16207293
#> 26 16214693
#> 27 16217062
#> 28 16224528
#> 29 16234309
#> 30 16244919
#> 31 16254612
#> 32 16258960
#> 33 16262035
#> 34 16262334
#> 35 16262336
#> 36 16262338
#> 37 16386749
#> 38 16386751
#> 39 16386752
#> 40 16400343
#> 41 16427771
#> 42 16439458
#> 43 16442170
#> 44 16549730
#> 45 16560460
#> 46 16560533
#> 47 16566547
#> 48 16566742
#> 49 16841646
#> 50 16845585
#> 51 16909478
#> 52 16909479
#> 53 16909480
#> 54 16909481
#> 55 16970638
#> 56 16973012
#> 57 17014255
#> 58 17051853
#> 59 17079499
#> 60 17113082
#> 61 17136539
#> 62 17154616
#> 63 17154616
#> 64 17157085
#> 65 17157085
#> 66 17157085
#> 67 17157085
#> 68 17157085
#> 69 17168884
#> 70 17172477
#> 71 17187665
#> 72 17187665
#> 73 17187977
#> 74 17209889
#> 75 17216769
#> 76 17216770
#> 77 17216771
#> 78 17216771
#> 79 17216789
#> 80 17216799
#> 81 17221295
#> 82 17302680
#> 83 17303055
#> 84 17326841
#> 85 17327911
#> 86 17331260
#> 87 17350100
#> 88 17375405
#> 89 17379581
#> 90 17379581
#> 91 17379581
#> 92 17379581
#> 93 17427850
#> 94 17429117
#> 95 17449676
#> 96 17466675
#> 97 17469609
#> 98 17469610
#> 99 17518422
#> 100 17523010
#> 101 17523010
#> 102 17577230
#> 103 17585626
#> 104 17585630
#> 105 17658972
#> 106 17667743
#> 107 17683132
#> 108 17683132
#> 109 17687818
#> 110 17706998
#> 111 17721525
#> 112 17721525
#> 113 17726847
#> 114 17734310
#> 115 17763207
#> 116 17765138
#> 117 17768872
#> 118 17768872
#> 119 17839567
#> 120 17839567
#> 121 17846396
#> 122 17860245
#> 123 17876770
#> 124 17876799
#> 125 17876802
#> 126 17876803
#> 127 17876805
#> 128 17876807
#> 129 17876808
#> 130 17876810
#> 131 17879807
#> 132 17880174
#> 133 17898107
#> 134 17898107
#> 135 17929265
#> 136 17929265
#> 137 17929265
#> 138 17949102
#> 139 17955812
#> 140 17967486
#> 141 17967486
#> 142 17967492
#> 143 17967494
#> 144 17977536
#> 145 17998075
#> 146 18001877
#> 147 18064272
#> 148 18150441
#> 149 18159414
#> 150 18160557
#> 151 18166484
#> 152 18173426
#> 153 18730960
#> 154 18731027
#> 155 18850784
#> alt
#> 1 A
#> 2 A
#> 3 C
#> 4 A
#> 5 CTTTTTCTTTCTTTCTTTTTCTTT
#> 6 TTTTCTTTTTCTTTC
#> 7 *
#> 8 ATTTCTTTTTCTTT
#> 9 CTTTTTCTTTTTCTTT
#> 10 TCTTCTTTCTTCCTTCCTTCCTTCCTTCCTTCCTCCCTTCCTTC
#> 11 A
#> 12 T
#> 13 T
#> 14 C
#> 15 C
#> 16 T
#> 17 T
#> 18 CA
#> 19 A
#> 20 CG
#> 21 T
#> 22 T
#> 23 G
#> 24 G
#> 25 G
#> 26 A
#> 27 G
#> 28 C
#> 29 T
#> 30 C
#> 31 AGAAGGAAGGAAGGAAA
#> 32 A
#> 33 A
#> 34 G
#> 35 *
#> 36 *
#> 37 *
#> 38 *
#> 39 CCCGCCGCCGCGGCTTTTTGCCCCCCACCCCCGCCGCCGCGGCTTTTTACCCGCCGCGGCTTTTTGCCCCCCCGCCGCCGTGGTTTTTTCCCCCCATCTCACCTCCGCTTTTTGCCCGCCGCGGCTTTTTGCCCCCACCCCGCCTCGGCTTTTTGCCAGCCACGGCTTTTTGCCCC
#> 40 C
#> 41 C
#> 42 G
#> 43 A
#> 44 G
#> 45 *
#> 46 CCAAGCCAGCCAAGTCAGCGAGCCAACCAAGCCAGCCAACTCAGCCAGCCACCTAAGCCAGCCAAGCCAGCCAGCCAGCCAAGCAAGCCAGCCAGCCAAGCCAGCCAAGCCAGCCAAGCCAGGCAGCCAGC
#> 47 *
#> 48 TAAGCCAGCCAGCTAGCCAAGCCACCCAGCCAGCCAGCCAGCCAAACCAGCCAAGCCAGCCAGCCAGCCAGCCAAGCCAGCCAAGCAAGCCAGCCAGCCAGCCAAGCCACGCAAGCCAGCCAGCCAGCCATGCCAGCCA
#> 49 AAAAAAAAAAAAAAA
#> 50 TCACA
#> 51 *
#> 52 CCCCTCTCTCTCTCTCTCTCTCCCT
#> 53 *
#> 54 *
#> 55 A
#> 56 A
#> 57 T
#> 58 T
#> 59 GAAAAAAAA
#> 60 A
#> 61 T
#> 62 CTTT
#> 63 CT
#> 64 CACACACAC
#> 65 T
#> 66 TACACACACACACACAC
#> 67 TACACACACACACACACACAC
#> 68 TACACACACACACACACACACACAC
#> 69 T
#> 70 T
#> 71 TA
#> 72 TAAA
#> 73 GC
#> 74 ATT
#> 75 ACAAAC
#> 76 ACAAC
#> 77 AC
#> 78 A
#> 79 CACAT
#> 80 T
#> 81 G
#> 82 A
#> 83 T
#> 84 C
#> 85 TACAC
#> 86 CT
#> 87 C
#> 88 G
#> 89 GGT
#> 90 GGTGTGT
#> 91 GGTGTGTGT
#> 92 GGTGTGTGTGT
#> 93 T
#> 94 A
#> 95 A
#> 96 T
#> 97 TCAGTAAGAATCCAGTTCTC
#> 98 CCA
#> 99 T
#> 100 AAAAAA
#> 101 GA
#> 102 A
#> 103 A
#> 104 *
#> 105 C
#> 106 A
#> 107 C
#> 108 CAAA
#> 109 C
#> 110 G
#> 111 ATTTTT
#> 112 AT
#> 113 A
#> 114 C
#> 115 G
#> 116 T
#> 117 CA
#> 118 CAAA
#> 119 CT
#> 120 CTT
#> 121 TA
#> 122 A
#> 123 GGTTATGGAGGTTAGGGAGGTTAGGGAAGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTAGGGAG
#> 124 *
#> 125 *
#> 126 *
#> 127 *
#> 128 *
#> 129 *
#> 130 *
#> 131 A
#> 132 A
#> 133 TA
#> 134 TAAA
#> 135 ATTTTTT
#> 136 ATTTTTTT
#> 137 ATTTTTTTT
#> 138 T
#> 139 A
#> 140 ACACACACC
#> 141 ACACACC
#> 142 ACACACACACC
#> 143 *
#> 144 TAA
#> 145 GTGAA
#> 146 C
#> 147 T
#> 148 C
#> 149 G
#> 150 C
#> 151 TGA
#> 152 A
#> 153 *
#> 154 C
#> 155 G
#> ref
#> 1 C
#> 2 C
#> 3 A
#> 4 G
#> 5 CTTTCTTTCTTTCTTTTTCTTT
#> 6 TTCTTTCTTTTTCTTTC
#> 7 TCTTTCTTTTTCTTTCTTC
#> 8 CTTTCTTTTTCTTT
#> 9 CTTTCTTTTTCTTT
#> 10 TTTCTTTCTTCCTTCCTTCCTTCCTTCCTTCCTCCCTTCCTTC
#> 11 G
#> 12 A
#> 13 C
#> 14 T
#> 15 T
#> 16 G
#> 17 C
#> 18 C
#> 19 C
#> 20 TG
#> 21 C
#> 22 C
#> 23 A
#> 24 A
#> 25 A
#> 26 C
#> 27 A
#> 28 T
#> 29 C
#> 30 T
#> 31 GGAAGGAAGGAAGGAAA
#> 32 C
#> 33 G
#> 34 GATTCCATTCGATGATTCCATTCA
#> 35 TTCCATTCGATGATTCCATTCAATTCCATTCGATGATGATTCCATTCGAG
#> 36 CCATTCGATGATTCCATTCAA
#> 37 TCCGCCGCCGCCGCGGCTTTTTGCCCCCCACCCCCGCCGCCGCGGCTTTTTACCCGCCGCGGCTTTTTGCCCCCCCGCCGCCGTGGTTTTTTCCCCCCATCTCACCTCCGCTTTTTGCCCGCCGCGGCTTTTTGCCCCCACCCCGCCTCGGCTTTTTGCCAGCCACGGCTTTTTGCCCCCCGCCACCGCGGCTTTTTGTCCC
#> 38 CGCCGCCGCCGCGGCTTTTTGCCCCCCACCCCCGCCGCCGCGGCTTTTTACCCGCCGCGGCTTTTTGCCCCCCCG
#> 39 GCCGCCGCCGCGGCTTTTTGCCCCCCACCCCCGCCGCCGCGGCTTTTTACCCGCCGCGGCTTTTTGCCCCCCCGCCGCCGTGGTTTTTTCCCCCCATCTCACCTCCGCTTTTTGCCCGCCGCGGCTTTTTGCCCCCACCCCGCCTCGGCTTTTTGCCAGCCACGGCTTTTTGCCCC
#> 40 T
#> 41 T
#> 42 A
#> 43 G
#> 44 A
#> 45 ACAGCCAGCCAGCCAAGCCAGCCAAGCCAGCCAGGAAAGCCAGCCTGCCAAGCCAGCCAAGCCAGCCAGCCACTCAAGCCAGCCAAGTCAGCGAGCCAACCAAGCCAGCCAACTCAGCCAGCCACCTAAGCCAGCCAAGCCAGCCAGCCAGCCAAGCAAGCCAGCCAGCCAAGCCAGCCAAGCCAGCCAAGCCAGGCAGCCAGCCAAGCCAGCCAAGCCAGCCAGCCAGCCAAGCCAGCCAGCCAGCCCACACAGCCAAGC
#> 46 TCAAGCCAGCCAAGTCAGCGAGCCAACCAAGCCAGCCAACTCAGCCAGCCACCTAAGCCAGCCAAGCCAGCCAGCCAGCCAAGCAAGCCAGCCAGCCAAGCCAGCCAAGCCAGCCAAGCCAGGCAGCCAGC
#> 47 ACAGCCAAGACAGCCAGCCAGCCACGCAAGCCAAGCCAGCCAGCCAGGCAAGCCAGGCATGCCAGCCAAGCCATCCAGCCAGCCAAGCCAGGCGGCCAGCCAAGCCAGCCAAGCCACCCGGCCAGCCAAGCCACCCAAGCCACCCGGCCAGCCAGGCATCCAAGCCAGCCAAGT
#> 48 CAAGCCAGCCAGCTAGCCAAGCCACCCAGCCAGCCAGCCAGCCAAACCAGCCAAGCCAGCCAGCCAGCCAGCCAAGCCAGCCAAGCAAGCCAGCCAGCCAGCCAAGCCACGCAAGCCAGCCAGCCAGCCATGCCAGCCA
#> 49 CAAAAAAAAAAAAAA
#> 50 TCA
#> 51 TCTCTCC
#> 52 CTCTCCCTCTCTCTCTCTCTCTCTCCCT
#> 53 TCTCCCTCTCTCTCTCTCTCTCTCC
#> 54 CTCCCTCTCTCTCTCTCTCTCTCCCT
#> 55 G
#> 56 G
#> 57 C
#> 58 C
#> 59 GAAAAAAA
#> 60 AG
#> 61 C
#> 62 CTT
#> 63 CTTT
#> 64 TACACACAC
#> 65 TACACACAC
#> 66 TACACACAC
#> 67 TACACACAC
#> 68 TACACACAC
#> 69 C
#> 70 C
#> 71 TAA
#> 72 TAA
#> 73 G
#> 74 AT
#> 75 AAAAC
#> 76 AAAC
#> 77 A
#> 78 C
#> 79 C
#> 80 G
#> 81 GT
#> 82 G
#> 83 C
#> 84 T
#> 85 TACACAC
#> 86 C
#> 87 T
#> 88 A
#> 89 GGTGT
#> 90 GGTGT
#> 91 GGTGT
#> 92 GGTGT
#> 93 G
#> 94 G
#> 95 C
#> 96 G
#> 97 TCCAGTAAGAATCCAGTTCTC
#> 98 TCA
#> 99 C
#> 100 GAAAAA
#> 101 GAAAAA
#> 102 G
#> 103 ATTTATT
#> 104 ATT
#> 105 T
#> 106 T
#> 107 CA
#> 108 CA
#> 109 CT
#> 110 A
#> 111 AT
#> 112 ATTTT
#> 113 G
#> 114 CTT
#> 115 A
#> 116 TCAAGACATCCTCCACAGAGGACC
#> 117 CAA
#> 118 CAA
#> 119 CTTT
#> 120 CTTT
#> 121 T
#> 122 C
#> 123 AGTTATGGAGGTTAGGGAGGTTAGGGAAGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTAGGGAG
#> 124 TTATGGAGGTTAGGGAGGTTAG
#> 125 TGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTAG
#> 126 GGAGGTTAGGGAGGTTAGGGAGGTTAT
#> 127 AGGTT
#> 128 GTTA
#> 129 TTAGG
#> 130 AGGGAGGTTAGGGAG
#> 131 G
#> 132 G
#> 133 TAA
#> 134 TAA
#> 135 ATTTTTTTTT
#> 136 ATTTTTTTTT
#> 137 ATTTTTTTTT
#> 138 C
#> 139 G
#> 140 A
#> 141 A
#> 142 ACCCACACACACC
#> 143 C
#> 144 TA
#> 145 G
#> 146 A
#> 147 A
#> 148 CA
#> 149 A
#> 150 T
#> 151 T
#> 152 C
#> 153 GTATACATAAGATATATTATATATAATATATTATATAAATGTATTATATATAACATATTATATATAATATATT
#> 154 T
#> 155 T
#>
#> attr(,"ldPanelsByRegion")$`/tmp/RtmpmBLZhq/pecotmr-ctwas-ld/2_chr22_2.ld`$variance
#> chr22:15574750:C:A
#> 0.15512823
#> chr22:15635104:C:A
#> 0.13875000
#> chr22:15689224:A:C
#> 0.49753766
#> chr22:15773180:G:A
#> 0.07986172
#> chr22:15837995:CTTTCTTTCTTTCTTTTTCTTT:CTTTTTCTTTCTTTCTTTTTCTTT
#> 0.07986172
#> chr22:15838001:TTCTTTCTTTTTCTTTC:TTTTCTTTTTCTTTC
#> 0.18000000
#> chr22:15838002:TCTTTCTTTTTCTTTCTTC:*
#> 0.18000000
#> chr22:15838003:CTTTCTTTTTCTTT:ATTTCTTTTTCTTT
#> 0.10986052
#> chr22:15838003:CTTTCTTTTTCTTT:CTTTTTCTTTTTCTTT
#> 0.16652832
#> chr22:15838010:TTTCTTTCTTCCTTCCTTCCTTCCTTCCTTCCTCCCTTCCTTC:TCTTCTTTCTTCCTTCCTTCCTTCCTTCCTTCCTCCCTTCCTTC
#> 0.19319392
#> chr22:15839920:G:A
#> 0.19319392
#> chr22:15919156:A:T
#> 0.42000000
#> chr22:15927084:C:T
#> 0.19319392
#> chr22:15947643:T:C
#> 0.10986052
#> chr22:15984722:T:C
#> 0.41319472
#> chr22:16073625:G:T
#> 0.19319392
#> chr22:16102937:C:T
#> 0.42652752
#> chr22:16111042:C:CA
#> 0.49875000
#> chr22:16112049:C:A
#> 0.45500000
#> chr22:16112091:TG:CG
#> 0.23111062
#> chr22:16115854:C:T
#> 0.49944442
#> chr22:16124912:C:T
#> 0.49652772
#> chr22:16132992:A:G
#> 0.49319452
#> chr22:16187126:A:G
#> 0.48875000
#> chr22:16207293:A:G
#> 0.36652812
#> chr22:16214693:C:A
#> 0.09500000
#> chr22:16217062:A:G
#> 0.49500000
#> chr22:16224528:T:C
#> 0.36652812
#> chr22:16234309:C:T
#> 0.49482917
#> chr22:16244919:T:C
#> 0.43277802
#> chr22:16254612:GGAAGGAAGGAAGGAAA:AGAAGGAAGGAAGGAAA
#> 0.14313283
#> chr22:16258960:C:A
#> 0.36652812
#> chr22:16262035:G:A
#> 0.36652812
#> chr22:16262334:GATTCCATTCGATGATTCCATTCA:G
#> 0.36652812
#> chr22:16262336:TTCCATTCGATGATTCCATTCAATTCCATTCGATGATGATTCCATTCGAG:*
#> 0.37500000
#> chr22:16262338:CCATTCGATGATTCCATTCAA:*
#> 0.36652812
#> chr22:16386749:TCCGCCGCCGCCGCGGCTTTTTGCCCCCCACCCCCGCCGCCGCGGCTTTTTACCCGCCGCGGCTTTTTGCCCCCCCGCCGCCGTGGTTTTTTCCCCCCATCTCACCTCCGCTTTTTGCCCGCCGCGGCTTTTTGCCCCCACCCCGCCTCGGCTTTTTGCCAGCCACGGCTTTTTGCCCCCCGCCACCGCGGCTTTTTGTCCC:*
#> 0.15755071
#> chr22:16386751:CGCCGCCGCCGCGGCTTTTTGCCCCCCACCCCCGCCGCCGCGGCTTTTTACCCGCCGCGGCTTTTTGCCCCCCCG:*
#> 0.11160580
#> chr22:16386752:GCCGCCGCCGCGGCTTTTTGCCCCCCACCCCCGCCGCCGCGGCTTTTTACCCGCCGCGGCTTTTTGCCCCCCCGCCGCCGTGGTTTTTTCCCCCCATCTCACCTCCGCTTTTTGCCCGCCGCGGCTTTTTGCCCCCACCCCGCCTCGGCTTTTTGCCAGCCACGGCTTTTTGCCCC:CCCGCCGCCGCGGCTTTTTGCCCCCCACCCCCGCCGCCGCGGCTTTTTACCCGCCGCGGCTTTTTGCCCCCCCGCCGCCGTGGTTTTTTCCCCCCATCTCACCTCCGCTTTTTGCCCGCCGCGGCTTTTTGCCCCCACCCCGCCTCGGCTTTTTGCCAGCCACGGCTTTTTGCCCC
#> 0.48513671
#> chr22:16400343:T:C
#> 0.21875000
#> chr22:16427771:T:C
#> 0.49875000
#> chr22:16439458:A:G
#> 0.23111062
#> chr22:16442170:G:A
#> 0.09500000
#> chr22:16549730:A:G
#> 0.10986052
#> chr22:16560460:ACAGCCAGCCAGCCAAGCCAGCCAAGCCAGCCAGGAAAGCCAGCCTGCCAAGCCAGCCAAGCCAGCCAGCCACTCAAGCCAGCCAAGTCAGCGAGCCAACCAAGCCAGCCAACTCAGCCAGCCACCTAAGCCAGCCAAGCCAGCCAGCCAGCCAAGCAAGCCAGCCAGCCAAGCCAGCCAAGCCAGCCAAGCCAGGCAGCCAGCCAAGCCAGCCAAGCCAGCCAGCCAGCCAAGCCAGCCAGCCAGCCCACACAGCCAAGC:*
#> 0.49482917
#> chr22:16560533:TCAAGCCAGCCAAGTCAGCGAGCCAACCAAGCCAGCCAACTCAGCCAGCCACCTAAGCCAGCCAAGCCAGCCAGCCAGCCAAGCAAGCCAGCCAGCCAAGCCAGCCAAGCCAGCCAAGCCAGGCAGCCAGC:CCAAGCCAGCCAAGTCAGCGAGCCAACCAAGCCAGCCAACTCAGCCAGCCACCTAAGCCAGCCAAGCCAGCCAGCCAGCCAAGCAAGCCAGCCAGCCAAGCCAGCCAAGCCAGCCAAGCCAGGCAGCCAGC
#> 0.09500000
#> chr22:16566547:ACAGCCAAGACAGCCAGCCAGCCACGCAAGCCAAGCCAGCCAGCCAGGCAAGCCAGGCATGCCAGCCAAGCCATCCAGCCAGCCAAGCCAGGCGGCCAGCCAAGCCAGCCAAGCCACCCGGCCAGCCAAGCCACCCAAGCCACCCGGCCAGCCAGGCATCCAAGCCAGCCAAGT:*
#> 0.25854588
#> chr22:16566742:CAAGCCAGCCAGCTAGCCAAGCCACCCAGCCAGCCAGCCAGCCAAACCAGCCAAGCCAGCCAGCCAGCCAGCCAAGCCAGCCAAGCAAGCCAGCCAGCCAGCCAAGCCACGCAAGCCAGCCAGCCAGCCATGCCAGCCA:TAAGCCAGCCAGCTAGCCAAGCCACCCAGCCAGCCAGCCAGCCAAACCAGCCAAGCCAGCCAGCCAGCCAGCCAAGCCAGCCAAGCAAGCCAGCCAGCCAGCCAAGCCACGCAAGCCAGCCAGCCAGCCATGCCAGCCA
#> 0.16652832
#> chr22:16841646:CAAAAAAAAAAAAAA:AAAAAAAAAAAAAAA
#> 0.07986172
#> chr22:16845585:TCA:TCACA
#> 0.36652812
#> chr22:16909478:TCTCTCC:*
#> 0.09652317
#> chr22:16909479:CTCTCCCTCTCTCTCTCTCTCTCTCCCT:CCCCTCTCTCTCTCTCTCTCTCCCT
#> 0.11160580
#> chr22:16909480:TCTCCCTCTCTCTCTCTCTCTCTCC:*
#> 0.09500000
#> chr22:16909481:CTCCCTCTCTCTCTCTCTCTCTCCCT:*
#> 0.09500000
#> chr22:16970638:G:A
#> 0.12444502
#> chr22:16973012:G:A
#> 0.13875000
#> chr22:17014255:C:T
#> 0.41319472
#> chr22:17051853:C:T
#> 0.33944482
#> chr22:17079499:GAAAAAAA:GAAAAAAAA
#> 0.38319412
#> chr22:17113082:AG:A
#> 0.10986052
#> chr22:17136539:C:T
#> 0.20206204
#> chr22:17154616:CTT:CTTT
#> 0.38319412
#> chr22:17154616:CTTT:CT
#> 0.15277722
#> chr22:17157085:TACACACAC:CACACACAC
#> 0.11160580
#> chr22:17157085:TACACACAC:T
#> 0.38738881
#> chr22:17157085:TACACACAC:TACACACACACACACAC
#> 0.43047951
#> chr22:17157085:TACACACAC:TACACACACACACACACACAC
#> 0.16906006
#> chr22:17157085:TACACACAC:TACACACACACACACACACACACAC
#> 0.14090747
#> chr22:17168884:C:T
#> 0.45500000
#> chr22:17172477:C:T
#> 0.37500000
#> chr22:17187665:TAA:TA
#> 0.13875000
#> chr22:17187665:TAA:TAAA
#> 0.37500000
#> chr22:17187977:G:GC
#> 0.16652832
#> chr22:17209889:AT:ATT
#> 0.20611162
#> chr22:17216769:AAAAC:ACAAAC
#> 0.13875000
#> chr22:17216770:AAAC:ACAAC
#> 0.18000000
#> chr22:17216771:A:AC
#> 0.22191952
#> chr22:17216771:C:A
#> 0.46322908
#> chr22:17216789:C:CACAT
#> 0.17436097
#> chr22:17216799:G:T
#> 0.16652832
#> chr22:17221295:GT:G
#> 0.37500000
#> chr22:17302680:G:A
#> 0.49652772
#> chr22:17303055:C:T
#> 0.49875000
#> chr22:17326841:T:C
#> 0.35777742
#> chr22:17327911:TACACAC:TACAC
#> 0.43277802
#> chr22:17331260:C:CT
#> 0.19319392
#> chr22:17350100:T:C
#> 0.49500000
#> chr22:17375405:A:G
#> 0.09500000
#> chr22:17379581:GGTGT:GGT
#> 0.10986052
#> chr22:17379581:GGTGT:GGTGTGT
#> 0.36652812
#> chr22:17379581:GGTGT:GGTGTGTGT
#> 0.28875000
#> chr22:17379581:GGTGT:GGTGTGTGTGT
#> 0.12444502
#> chr22:17427850:G:T
#> 0.49944442
#> chr22:17429117:G:A
#> 0.49986112
#> chr22:17449676:C:A
#> 0.25500000
#> chr22:17466675:G:T
#> 0.24319492
#> chr22:17469609:TCCAGTAAGAATCCAGTTCTC:TCAGTAAGAATCCAGTTCTC
#> 0.28875000
#> chr22:17469610:TCA:CCA
#> 0.47652792
#> chr22:17518422:C:T
#> 0.28875000
#> chr22:17523010:GAAAAA:AAAAAA
#> 0.18000000
#> chr22:17523010:GAAAAA:GA
#> 0.29944402
#> chr22:17577230:G:A
#> 0.09500000
#> chr22:17585626:ATTTATT:A
#> 0.25500000
#> chr22:17585630:ATT:*
#> 0.25500000
#> chr22:17658972:T:C
#> 0.17167130
#> chr22:17667743:T:A
#> 0.07986172
#> chr22:17683132:CA:C
#> 0.15277722
#> chr22:17683132:CA:CAAA
#> 0.29944402
#> chr22:17687818:CT:C
#> 0.37920110
#> chr22:17706998:A:G
#> 0.12444502
#> chr22:17721525:AT:ATTTTT
#> 0.12841938
#> chr22:17721525:ATTTT:AT
#> 0.37500000
#> chr22:17726847:G:A
#> 0.49500000
#> chr22:17734310:CTT:C
#> 0.29944402
#> chr22:17763207:A:G
#> 0.49875000
#> chr22:17765138:TCAAGACATCCTCCACAGAGGACC:T
#> 0.16652832
#> chr22:17768872:CAA:CA
#> 0.12841938
#> chr22:17768872:CAA:CAAA
#> 0.23781208
#> chr22:17839567:CTTT:CT
#> 0.37500000
#> chr22:17839567:CTTT:CTT
#> 0.09500000
#> chr22:17846396:T:TA
#> 0.32000000
#> chr22:17860245:C:A
#> 0.46444462
#> chr22:17876770:AGTTATGGAGGTTAGGGAGGTTAGGGAAGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTAGGGAG:GGTTATGGAGGTTAGGGAGGTTAGGGAAGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTAGGGAG
#> 0.08249026
#> chr22:17876799:TTATGGAGGTTAGGGAGGTTAG:*
#> 0.10986052
#> chr22:17876802:TGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTAG:*
#> 0.10986052
#> chr22:17876803:GGAGGTTAGGGAGGTTAGGGAGGTTAT:*
#> 0.13875000
#> chr22:17876805:AGGTT:*
#> 0.12444502
#> chr22:17876807:GTTA:*
#> 0.12444502
#> chr22:17876808:TTAGG:*
#> 0.12444502
#> chr22:17876810:AGGGAGGTTAGGGAG:*
#> 0.11160580
#> chr22:17879807:G:A
#> 0.13875000
#> chr22:17880174:G:A
#> 0.33944482
#> chr22:17898107:TAA:TA
#> 0.23111062
#> chr22:17898107:TAA:TAAA
#> 0.44444422
#> chr22:17929265:ATTTTTTTTT:ATTTTTT
#> 0.09500000
#> chr22:17929265:ATTTTTTTTT:ATTTTTTT
#> 0.38319412
#> chr22:17929265:ATTTTTTTTT:ATTTTTTTT
#> 0.49319452
#> chr22:17949102:C:T
#> 0.12444502
#> chr22:17955812:G:A
#> 0.32000000
#> chr22:17967486:A:ACACACACC
#> 0.26652732
#> chr22:17967486:A:ACACACC
#> 0.09500000
#> chr22:17967492:ACCCACACACACC:ACACACACACC
#> 0.32000000
#> chr22:17967494:C:*
#> 0.32000000
#> chr22:17977536:TA:TAA
#> 0.35777742
#> chr22:17998075:G:GTGAA
#> 0.35777742
#> chr22:18001877:A:C
#> 0.49652772
#> chr22:18064272:A:T
#> 0.30986152
#> chr22:18150441:CA:C
#> 0.23111062
#> chr22:18159414:A:G
#> 0.28875000
#> chr22:18160557:T:C
#> 0.34875000
#> chr22:18166484:T:TGA
#> 0.09500000
#> chr22:18173426:C:A
#> 0.23111062
#> chr22:18730960:GTATACATAAGATATATTATATATAATATATTATATAAATGTATTATATATAACATATTATATATAATATATT:*
#> 0.15755071
#> chr22:18731027:T:C
#> 0.08115506
#> chr22:18850784:T:G
#> 0.12444502
#>
#> attr(,"ldPanelsByRegion")$`/tmp/RtmpmBLZhq/pecotmr-ctwas-ld/2_chr22_2.ld`$sketch
#> class: RangedSummarizedExperiment
#> dim: 155 1000
#> metadata(2): genotypeSource ldProjection
#> assays(1): dosage
#> rownames(155): chr22:15574750:C:A chr22:15635104:C:A ...
#> chr22:18731027:T:C chr22:18850784:T:G
#> rowData names(4): SNP A1 A2 AF
#> colnames(1000): S1 S2 ... S999 S1000
#> colData names(0):
#>
#>
#>
#> $snpinfo_loader_fun
#> function (LD_file)
#> {
#> .ctwasLoaderPanel(sys.function(), LD_file, "snpInfo loader")$snpInfo
#> }
#> <bytecode: 0x559e986fb868>
#> <environment: namespace:pecotmr>
#> attr(,"ldPanelsByRegion")
#> attr(,"ldPanelsByRegion")$`/tmp/RtmpmBLZhq/pecotmr-ctwas-ld/1_chr22_1.ld`
#> attr(,"ldPanelsByRegion")$`/tmp/RtmpmBLZhq/pecotmr-ctwas-ld/1_chr22_1.ld`$snpInfo
#> chrom id pos alt
#> 1 22 chr22:10685239:C:T 10685239 T
#> 2 22 chr22:10761227:G:A 10761227 A
#> 3 22 chr22:11285239:C:T 11285239 T
#> 4 22 chr22:11601805:G:A 11601805 A
#> 5 22 chr22:11791698:G:T 11791698 T
#> 6 22 chr22:11797697:C:T 11797697 T
#> 7 22 chr22:12044872:A:C 12044872 C
#> 8 22 chr22:12194389:G:A 12194389 A
#> 9 22 chr22:12207043:C:T 12207043 T
#> 10 22 chr22:12350816:G:A 12350816 A
#> 11 22 chr22:12352464:C:A 12352464 A
#> 12 22 chr22:12370627:C:T 12370627 T
#> 13 22 chr22:12383838:G:A 12383838 A
#> 14 22 chr22:12571373:AGAAAGAAAGAAAGAAAGAAG:* 12571373 *
#> 15 22 chr22:12571377:AGAAAGAAAGAAAGAAG:* 12571377 *
#> 16 22 chr22:12571385:AGAAAGAAG:* 12571385 *
#> 17 22 chr22:12571386:GAAAGAAGGA:* 12571386 *
#> 18 22 chr22:12571389:AGAAGGAAAGAAGGAAAGAAAGGAAGAAGGAAAGAAG:* 12571389 *
#> 19 22 chr22:12576050:T:A 12576050 A
#> 20 22 chr22:12640661:G:T 12640661 T
#> ref
#> 1 C
#> 2 G
#> 3 C
#> 4 G
#> 5 G
#> 6 C
#> 7 A
#> 8 G
#> 9 C
#> 10 G
#> 11 C
#> 12 C
#> 13 G
#> 14 AGAAAGAAAGAAAGAAAGAAG
#> 15 AGAAAGAAAGAAAGAAG
#> 16 AGAAAGAAG
#> 17 GAAAGAAGGA
#> 18 AGAAGGAAAGAAGGAAAGAAAGGAAGAAGGAAAGAAG
#> 19 T
#> 20 G
#>
#> attr(,"ldPanelsByRegion")$`/tmp/RtmpmBLZhq/pecotmr-ctwas-ld/1_chr22_1.ld`$variance
#> chr22:10685239:C:T
#> 0.10986052
#> chr22:10761227:G:A
#> 0.25500000
#> chr22:11285239:C:T
#> 0.15277722
#> chr22:11601805:G:A
#> 0.10986052
#> chr22:11791698:G:T
#> 0.09500000
#> chr22:11797697:C:T
#> 0.09500000
#> chr22:12044872:A:C
#> 0.07986172
#> chr22:12194389:G:A
#> 0.10986052
#> chr22:12207043:C:T
#> 0.10986052
#> chr22:12350816:G:A
#> 0.10986052
#> chr22:12352464:C:A
#> 0.21875000
#> chr22:12370627:C:T
#> 0.21875000
#> chr22:12383838:G:A
#> 0.07986172
#> chr22:12571373:AGAAAGAAAGAAAGAAAGAAG:*
#> 0.20611162
#> chr22:12571377:AGAAAGAAAGAAAGAAG:*
#> 0.19319392
#> chr22:12571385:AGAAAGAAG:*
#> 0.16652832
#> chr22:12571386:GAAAGAAGGA:*
#> 0.16652832
#> chr22:12571389:AGAAGGAAAGAAGGAAAGAAAGGAAGAAGGAAAGAAG:*
#> 0.16652832
#> chr22:12576050:T:A
#> 0.21875000
#> chr22:12640661:G:T
#> 0.18000000
#>
#> attr(,"ldPanelsByRegion")$`/tmp/RtmpmBLZhq/pecotmr-ctwas-ld/1_chr22_1.ld`$sketch
#> class: RangedSummarizedExperiment
#> dim: 20 1000
#> metadata(2): genotypeSource ldProjection
#> assays(1): dosage
#> rownames(20): chr22:10685239:C:T chr22:10761227:G:A ...
#> chr22:12576050:T:A chr22:12640661:G:T
#> rowData names(4): SNP A1 A2 AF
#> colnames(1000): S1 S2 ... S999 S1000
#> colData names(0):
#>
#>
#> attr(,"ldPanelsByRegion")$`/tmp/RtmpmBLZhq/pecotmr-ctwas-ld/2_chr22_2.ld`
#> attr(,"ldPanelsByRegion")$`/tmp/RtmpmBLZhq/pecotmr-ctwas-ld/2_chr22_2.ld`$snpInfo
#> chrom
#> 1 22
#> 2 22
#> 3 22
#> 4 22
#> 5 22
#> 6 22
#> 7 22
#> 8 22
#> 9 22
#> 10 22
#> 11 22
#> 12 22
#> 13 22
#> 14 22
#> 15 22
#> 16 22
#> 17 22
#> 18 22
#> 19 22
#> 20 22
#> 21 22
#> 22 22
#> 23 22
#> 24 22
#> 25 22
#> 26 22
#> 27 22
#> 28 22
#> 29 22
#> 30 22
#> 31 22
#> 32 22
#> 33 22
#> 34 22
#> 35 22
#> 36 22
#> 37 22
#> 38 22
#> 39 22
#> 40 22
#> 41 22
#> 42 22
#> 43 22
#> 44 22
#> 45 22
#> 46 22
#> 47 22
#> 48 22
#> 49 22
#> 50 22
#> 51 22
#> 52 22
#> 53 22
#> 54 22
#> 55 22
#> 56 22
#> 57 22
#> 58 22
#> 59 22
#> 60 22
#> 61 22
#> 62 22
#> 63 22
#> 64 22
#> 65 22
#> 66 22
#> 67 22
#> 68 22
#> 69 22
#> 70 22
#> 71 22
#> 72 22
#> 73 22
#> 74 22
#> 75 22
#> 76 22
#> 77 22
#> 78 22
#> 79 22
#> 80 22
#> 81 22
#> 82 22
#> 83 22
#> 84 22
#> 85 22
#> 86 22
#> 87 22
#> 88 22
#> 89 22
#> 90 22
#> 91 22
#> 92 22
#> 93 22
#> 94 22
#> 95 22
#> 96 22
#> 97 22
#> 98 22
#> 99 22
#> 100 22
#> 101 22
#> 102 22
#> 103 22
#> 104 22
#> 105 22
#> 106 22
#> 107 22
#> 108 22
#> 109 22
#> 110 22
#> 111 22
#> 112 22
#> 113 22
#> 114 22
#> 115 22
#> 116 22
#> 117 22
#> 118 22
#> 119 22
#> 120 22
#> 121 22
#> 122 22
#> 123 22
#> 124 22
#> 125 22
#> 126 22
#> 127 22
#> 128 22
#> 129 22
#> 130 22
#> 131 22
#> 132 22
#> 133 22
#> 134 22
#> 135 22
#> 136 22
#> 137 22
#> 138 22
#> 139 22
#> 140 22
#> 141 22
#> 142 22
#> 143 22
#> 144 22
#> 145 22
#> 146 22
#> 147 22
#> 148 22
#> 149 22
#> 150 22
#> 151 22
#> 152 22
#> 153 22
#> 154 22
#> 155 22
#> id
#> 1 chr22:15574750:C:A
#> 2 chr22:15635104:C:A
#> 3 chr22:15689224:A:C
#> 4 chr22:15773180:G:A
#> 5 chr22:15837995:CTTTCTTTCTTTCTTTTTCTTT:CTTTTTCTTTCTTTCTTTTTCTTT
#> 6 chr22:15838001:TTCTTTCTTTTTCTTTC:TTTTCTTTTTCTTTC
#> 7 chr22:15838002:TCTTTCTTTTTCTTTCTTC:*
#> 8 chr22:15838003:CTTTCTTTTTCTTT:ATTTCTTTTTCTTT
#> 9 chr22:15838003:CTTTCTTTTTCTTT:CTTTTTCTTTTTCTTT
#> 10 chr22:15838010:TTTCTTTCTTCCTTCCTTCCTTCCTTCCTTCCTCCCTTCCTTC:TCTTCTTTCTTCCTTCCTTCCTTCCTTCCTTCCTCCCTTCCTTC
#> 11 chr22:15839920:G:A
#> 12 chr22:15919156:A:T
#> 13 chr22:15927084:C:T
#> 14 chr22:15947643:T:C
#> 15 chr22:15984722:T:C
#> 16 chr22:16073625:G:T
#> 17 chr22:16102937:C:T
#> 18 chr22:16111042:C:CA
#> 19 chr22:16112049:C:A
#> 20 chr22:16112091:TG:CG
#> 21 chr22:16115854:C:T
#> 22 chr22:16124912:C:T
#> 23 chr22:16132992:A:G
#> 24 chr22:16187126:A:G
#> 25 chr22:16207293:A:G
#> 26 chr22:16214693:C:A
#> 27 chr22:16217062:A:G
#> 28 chr22:16224528:T:C
#> 29 chr22:16234309:C:T
#> 30 chr22:16244919:T:C
#> 31 chr22:16254612:GGAAGGAAGGAAGGAAA:AGAAGGAAGGAAGGAAA
#> 32 chr22:16258960:C:A
#> 33 chr22:16262035:G:A
#> 34 chr22:16262334:GATTCCATTCGATGATTCCATTCA:G
#> 35 chr22:16262336:TTCCATTCGATGATTCCATTCAATTCCATTCGATGATGATTCCATTCGAG:*
#> 36 chr22:16262338:CCATTCGATGATTCCATTCAA:*
#> 37 chr22:16386749:TCCGCCGCCGCCGCGGCTTTTTGCCCCCCACCCCCGCCGCCGCGGCTTTTTACCCGCCGCGGCTTTTTGCCCCCCCGCCGCCGTGGTTTTTTCCCCCCATCTCACCTCCGCTTTTTGCCCGCCGCGGCTTTTTGCCCCCACCCCGCCTCGGCTTTTTGCCAGCCACGGCTTTTTGCCCCCCGCCACCGCGGCTTTTTGTCCC:*
#> 38 chr22:16386751:CGCCGCCGCCGCGGCTTTTTGCCCCCCACCCCCGCCGCCGCGGCTTTTTACCCGCCGCGGCTTTTTGCCCCCCCG:*
#> 39 chr22:16386752:GCCGCCGCCGCGGCTTTTTGCCCCCCACCCCCGCCGCCGCGGCTTTTTACCCGCCGCGGCTTTTTGCCCCCCCGCCGCCGTGGTTTTTTCCCCCCATCTCACCTCCGCTTTTTGCCCGCCGCGGCTTTTTGCCCCCACCCCGCCTCGGCTTTTTGCCAGCCACGGCTTTTTGCCCC:CCCGCCGCCGCGGCTTTTTGCCCCCCACCCCCGCCGCCGCGGCTTTTTACCCGCCGCGGCTTTTTGCCCCCCCGCCGCCGTGGTTTTTTCCCCCCATCTCACCTCCGCTTTTTGCCCGCCGCGGCTTTTTGCCCCCACCCCGCCTCGGCTTTTTGCCAGCCACGGCTTTTTGCCCC
#> 40 chr22:16400343:T:C
#> 41 chr22:16427771:T:C
#> 42 chr22:16439458:A:G
#> 43 chr22:16442170:G:A
#> 44 chr22:16549730:A:G
#> 45 chr22:16560460:ACAGCCAGCCAGCCAAGCCAGCCAAGCCAGCCAGGAAAGCCAGCCTGCCAAGCCAGCCAAGCCAGCCAGCCACTCAAGCCAGCCAAGTCAGCGAGCCAACCAAGCCAGCCAACTCAGCCAGCCACCTAAGCCAGCCAAGCCAGCCAGCCAGCCAAGCAAGCCAGCCAGCCAAGCCAGCCAAGCCAGCCAAGCCAGGCAGCCAGCCAAGCCAGCCAAGCCAGCCAGCCAGCCAAGCCAGCCAGCCAGCCCACACAGCCAAGC:*
#> 46 chr22:16560533:TCAAGCCAGCCAAGTCAGCGAGCCAACCAAGCCAGCCAACTCAGCCAGCCACCTAAGCCAGCCAAGCCAGCCAGCCAGCCAAGCAAGCCAGCCAGCCAAGCCAGCCAAGCCAGCCAAGCCAGGCAGCCAGC:CCAAGCCAGCCAAGTCAGCGAGCCAACCAAGCCAGCCAACTCAGCCAGCCACCTAAGCCAGCCAAGCCAGCCAGCCAGCCAAGCAAGCCAGCCAGCCAAGCCAGCCAAGCCAGCCAAGCCAGGCAGCCAGC
#> 47 chr22:16566547:ACAGCCAAGACAGCCAGCCAGCCACGCAAGCCAAGCCAGCCAGCCAGGCAAGCCAGGCATGCCAGCCAAGCCATCCAGCCAGCCAAGCCAGGCGGCCAGCCAAGCCAGCCAAGCCACCCGGCCAGCCAAGCCACCCAAGCCACCCGGCCAGCCAGGCATCCAAGCCAGCCAAGT:*
#> 48 chr22:16566742:CAAGCCAGCCAGCTAGCCAAGCCACCCAGCCAGCCAGCCAGCCAAACCAGCCAAGCCAGCCAGCCAGCCAGCCAAGCCAGCCAAGCAAGCCAGCCAGCCAGCCAAGCCACGCAAGCCAGCCAGCCAGCCATGCCAGCCA:TAAGCCAGCCAGCTAGCCAAGCCACCCAGCCAGCCAGCCAGCCAAACCAGCCAAGCCAGCCAGCCAGCCAGCCAAGCCAGCCAAGCAAGCCAGCCAGCCAGCCAAGCCACGCAAGCCAGCCAGCCAGCCATGCCAGCCA
#> 49 chr22:16841646:CAAAAAAAAAAAAAA:AAAAAAAAAAAAAAA
#> 50 chr22:16845585:TCA:TCACA
#> 51 chr22:16909478:TCTCTCC:*
#> 52 chr22:16909479:CTCTCCCTCTCTCTCTCTCTCTCTCCCT:CCCCTCTCTCTCTCTCTCTCTCCCT
#> 53 chr22:16909480:TCTCCCTCTCTCTCTCTCTCTCTCC:*
#> 54 chr22:16909481:CTCCCTCTCTCTCTCTCTCTCTCCCT:*
#> 55 chr22:16970638:G:A
#> 56 chr22:16973012:G:A
#> 57 chr22:17014255:C:T
#> 58 chr22:17051853:C:T
#> 59 chr22:17079499:GAAAAAAA:GAAAAAAAA
#> 60 chr22:17113082:AG:A
#> 61 chr22:17136539:C:T
#> 62 chr22:17154616:CTT:CTTT
#> 63 chr22:17154616:CTTT:CT
#> 64 chr22:17157085:TACACACAC:CACACACAC
#> 65 chr22:17157085:TACACACAC:T
#> 66 chr22:17157085:TACACACAC:TACACACACACACACAC
#> 67 chr22:17157085:TACACACAC:TACACACACACACACACACAC
#> 68 chr22:17157085:TACACACAC:TACACACACACACACACACACACAC
#> 69 chr22:17168884:C:T
#> 70 chr22:17172477:C:T
#> 71 chr22:17187665:TAA:TA
#> 72 chr22:17187665:TAA:TAAA
#> 73 chr22:17187977:G:GC
#> 74 chr22:17209889:AT:ATT
#> 75 chr22:17216769:AAAAC:ACAAAC
#> 76 chr22:17216770:AAAC:ACAAC
#> 77 chr22:17216771:A:AC
#> 78 chr22:17216771:C:A
#> 79 chr22:17216789:C:CACAT
#> 80 chr22:17216799:G:T
#> 81 chr22:17221295:GT:G
#> 82 chr22:17302680:G:A
#> 83 chr22:17303055:C:T
#> 84 chr22:17326841:T:C
#> 85 chr22:17327911:TACACAC:TACAC
#> 86 chr22:17331260:C:CT
#> 87 chr22:17350100:T:C
#> 88 chr22:17375405:A:G
#> 89 chr22:17379581:GGTGT:GGT
#> 90 chr22:17379581:GGTGT:GGTGTGT
#> 91 chr22:17379581:GGTGT:GGTGTGTGT
#> 92 chr22:17379581:GGTGT:GGTGTGTGTGT
#> 93 chr22:17427850:G:T
#> 94 chr22:17429117:G:A
#> 95 chr22:17449676:C:A
#> 96 chr22:17466675:G:T
#> 97 chr22:17469609:TCCAGTAAGAATCCAGTTCTC:TCAGTAAGAATCCAGTTCTC
#> 98 chr22:17469610:TCA:CCA
#> 99 chr22:17518422:C:T
#> 100 chr22:17523010:GAAAAA:AAAAAA
#> 101 chr22:17523010:GAAAAA:GA
#> 102 chr22:17577230:G:A
#> 103 chr22:17585626:ATTTATT:A
#> 104 chr22:17585630:ATT:*
#> 105 chr22:17658972:T:C
#> 106 chr22:17667743:T:A
#> 107 chr22:17683132:CA:C
#> 108 chr22:17683132:CA:CAAA
#> 109 chr22:17687818:CT:C
#> 110 chr22:17706998:A:G
#> 111 chr22:17721525:AT:ATTTTT
#> 112 chr22:17721525:ATTTT:AT
#> 113 chr22:17726847:G:A
#> 114 chr22:17734310:CTT:C
#> 115 chr22:17763207:A:G
#> 116 chr22:17765138:TCAAGACATCCTCCACAGAGGACC:T
#> 117 chr22:17768872:CAA:CA
#> 118 chr22:17768872:CAA:CAAA
#> 119 chr22:17839567:CTTT:CT
#> 120 chr22:17839567:CTTT:CTT
#> 121 chr22:17846396:T:TA
#> 122 chr22:17860245:C:A
#> 123 chr22:17876770:AGTTATGGAGGTTAGGGAGGTTAGGGAAGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTAGGGAG:GGTTATGGAGGTTAGGGAGGTTAGGGAAGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTAGGGAG
#> 124 chr22:17876799:TTATGGAGGTTAGGGAGGTTAG:*
#> 125 chr22:17876802:TGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTAG:*
#> 126 chr22:17876803:GGAGGTTAGGGAGGTTAGGGAGGTTAT:*
#> 127 chr22:17876805:AGGTT:*
#> 128 chr22:17876807:GTTA:*
#> 129 chr22:17876808:TTAGG:*
#> 130 chr22:17876810:AGGGAGGTTAGGGAG:*
#> 131 chr22:17879807:G:A
#> 132 chr22:17880174:G:A
#> 133 chr22:17898107:TAA:TA
#> 134 chr22:17898107:TAA:TAAA
#> 135 chr22:17929265:ATTTTTTTTT:ATTTTTT
#> 136 chr22:17929265:ATTTTTTTTT:ATTTTTTT
#> 137 chr22:17929265:ATTTTTTTTT:ATTTTTTTT
#> 138 chr22:17949102:C:T
#> 139 chr22:17955812:G:A
#> 140 chr22:17967486:A:ACACACACC
#> 141 chr22:17967486:A:ACACACC
#> 142 chr22:17967492:ACCCACACACACC:ACACACACACC
#> 143 chr22:17967494:C:*
#> 144 chr22:17977536:TA:TAA
#> 145 chr22:17998075:G:GTGAA
#> 146 chr22:18001877:A:C
#> 147 chr22:18064272:A:T
#> 148 chr22:18150441:CA:C
#> 149 chr22:18159414:A:G
#> 150 chr22:18160557:T:C
#> 151 chr22:18166484:T:TGA
#> 152 chr22:18173426:C:A
#> 153 chr22:18730960:GTATACATAAGATATATTATATATAATATATTATATAAATGTATTATATATAACATATTATATATAATATATT:*
#> 154 chr22:18731027:T:C
#> 155 chr22:18850784:T:G
#> pos
#> 1 15574750
#> 2 15635104
#> 3 15689224
#> 4 15773180
#> 5 15837995
#> 6 15838001
#> 7 15838002
#> 8 15838003
#> 9 15838003
#> 10 15838010
#> 11 15839920
#> 12 15919156
#> 13 15927084
#> 14 15947643
#> 15 15984722
#> 16 16073625
#> 17 16102937
#> 18 16111042
#> 19 16112049
#> 20 16112091
#> 21 16115854
#> 22 16124912
#> 23 16132992
#> 24 16187126
#> 25 16207293
#> 26 16214693
#> 27 16217062
#> 28 16224528
#> 29 16234309
#> 30 16244919
#> 31 16254612
#> 32 16258960
#> 33 16262035
#> 34 16262334
#> 35 16262336
#> 36 16262338
#> 37 16386749
#> 38 16386751
#> 39 16386752
#> 40 16400343
#> 41 16427771
#> 42 16439458
#> 43 16442170
#> 44 16549730
#> 45 16560460
#> 46 16560533
#> 47 16566547
#> 48 16566742
#> 49 16841646
#> 50 16845585
#> 51 16909478
#> 52 16909479
#> 53 16909480
#> 54 16909481
#> 55 16970638
#> 56 16973012
#> 57 17014255
#> 58 17051853
#> 59 17079499
#> 60 17113082
#> 61 17136539
#> 62 17154616
#> 63 17154616
#> 64 17157085
#> 65 17157085
#> 66 17157085
#> 67 17157085
#> 68 17157085
#> 69 17168884
#> 70 17172477
#> 71 17187665
#> 72 17187665
#> 73 17187977
#> 74 17209889
#> 75 17216769
#> 76 17216770
#> 77 17216771
#> 78 17216771
#> 79 17216789
#> 80 17216799
#> 81 17221295
#> 82 17302680
#> 83 17303055
#> 84 17326841
#> 85 17327911
#> 86 17331260
#> 87 17350100
#> 88 17375405
#> 89 17379581
#> 90 17379581
#> 91 17379581
#> 92 17379581
#> 93 17427850
#> 94 17429117
#> 95 17449676
#> 96 17466675
#> 97 17469609
#> 98 17469610
#> 99 17518422
#> 100 17523010
#> 101 17523010
#> 102 17577230
#> 103 17585626
#> 104 17585630
#> 105 17658972
#> 106 17667743
#> 107 17683132
#> 108 17683132
#> 109 17687818
#> 110 17706998
#> 111 17721525
#> 112 17721525
#> 113 17726847
#> 114 17734310
#> 115 17763207
#> 116 17765138
#> 117 17768872
#> 118 17768872
#> 119 17839567
#> 120 17839567
#> 121 17846396
#> 122 17860245
#> 123 17876770
#> 124 17876799
#> 125 17876802
#> 126 17876803
#> 127 17876805
#> 128 17876807
#> 129 17876808
#> 130 17876810
#> 131 17879807
#> 132 17880174
#> 133 17898107
#> 134 17898107
#> 135 17929265
#> 136 17929265
#> 137 17929265
#> 138 17949102
#> 139 17955812
#> 140 17967486
#> 141 17967486
#> 142 17967492
#> 143 17967494
#> 144 17977536
#> 145 17998075
#> 146 18001877
#> 147 18064272
#> 148 18150441
#> 149 18159414
#> 150 18160557
#> 151 18166484
#> 152 18173426
#> 153 18730960
#> 154 18731027
#> 155 18850784
#> alt
#> 1 A
#> 2 A
#> 3 C
#> 4 A
#> 5 CTTTTTCTTTCTTTCTTTTTCTTT
#> 6 TTTTCTTTTTCTTTC
#> 7 *
#> 8 ATTTCTTTTTCTTT
#> 9 CTTTTTCTTTTTCTTT
#> 10 TCTTCTTTCTTCCTTCCTTCCTTCCTTCCTTCCTCCCTTCCTTC
#> 11 A
#> 12 T
#> 13 T
#> 14 C
#> 15 C
#> 16 T
#> 17 T
#> 18 CA
#> 19 A
#> 20 CG
#> 21 T
#> 22 T
#> 23 G
#> 24 G
#> 25 G
#> 26 A
#> 27 G
#> 28 C
#> 29 T
#> 30 C
#> 31 AGAAGGAAGGAAGGAAA
#> 32 A
#> 33 A
#> 34 G
#> 35 *
#> 36 *
#> 37 *
#> 38 *
#> 39 CCCGCCGCCGCGGCTTTTTGCCCCCCACCCCCGCCGCCGCGGCTTTTTACCCGCCGCGGCTTTTTGCCCCCCCGCCGCCGTGGTTTTTTCCCCCCATCTCACCTCCGCTTTTTGCCCGCCGCGGCTTTTTGCCCCCACCCCGCCTCGGCTTTTTGCCAGCCACGGCTTTTTGCCCC
#> 40 C
#> 41 C
#> 42 G
#> 43 A
#> 44 G
#> 45 *
#> 46 CCAAGCCAGCCAAGTCAGCGAGCCAACCAAGCCAGCCAACTCAGCCAGCCACCTAAGCCAGCCAAGCCAGCCAGCCAGCCAAGCAAGCCAGCCAGCCAAGCCAGCCAAGCCAGCCAAGCCAGGCAGCCAGC
#> 47 *
#> 48 TAAGCCAGCCAGCTAGCCAAGCCACCCAGCCAGCCAGCCAGCCAAACCAGCCAAGCCAGCCAGCCAGCCAGCCAAGCCAGCCAAGCAAGCCAGCCAGCCAGCCAAGCCACGCAAGCCAGCCAGCCAGCCATGCCAGCCA
#> 49 AAAAAAAAAAAAAAA
#> 50 TCACA
#> 51 *
#> 52 CCCCTCTCTCTCTCTCTCTCTCCCT
#> 53 *
#> 54 *
#> 55 A
#> 56 A
#> 57 T
#> 58 T
#> 59 GAAAAAAAA
#> 60 A
#> 61 T
#> 62 CTTT
#> 63 CT
#> 64 CACACACAC
#> 65 T
#> 66 TACACACACACACACAC
#> 67 TACACACACACACACACACAC
#> 68 TACACACACACACACACACACACAC
#> 69 T
#> 70 T
#> 71 TA
#> 72 TAAA
#> 73 GC
#> 74 ATT
#> 75 ACAAAC
#> 76 ACAAC
#> 77 AC
#> 78 A
#> 79 CACAT
#> 80 T
#> 81 G
#> 82 A
#> 83 T
#> 84 C
#> 85 TACAC
#> 86 CT
#> 87 C
#> 88 G
#> 89 GGT
#> 90 GGTGTGT
#> 91 GGTGTGTGT
#> 92 GGTGTGTGTGT
#> 93 T
#> 94 A
#> 95 A
#> 96 T
#> 97 TCAGTAAGAATCCAGTTCTC
#> 98 CCA
#> 99 T
#> 100 AAAAAA
#> 101 GA
#> 102 A
#> 103 A
#> 104 *
#> 105 C
#> 106 A
#> 107 C
#> 108 CAAA
#> 109 C
#> 110 G
#> 111 ATTTTT
#> 112 AT
#> 113 A
#> 114 C
#> 115 G
#> 116 T
#> 117 CA
#> 118 CAAA
#> 119 CT
#> 120 CTT
#> 121 TA
#> 122 A
#> 123 GGTTATGGAGGTTAGGGAGGTTAGGGAAGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTAGGGAG
#> 124 *
#> 125 *
#> 126 *
#> 127 *
#> 128 *
#> 129 *
#> 130 *
#> 131 A
#> 132 A
#> 133 TA
#> 134 TAAA
#> 135 ATTTTTT
#> 136 ATTTTTTT
#> 137 ATTTTTTTT
#> 138 T
#> 139 A
#> 140 ACACACACC
#> 141 ACACACC
#> 142 ACACACACACC
#> 143 *
#> 144 TAA
#> 145 GTGAA
#> 146 C
#> 147 T
#> 148 C
#> 149 G
#> 150 C
#> 151 TGA
#> 152 A
#> 153 *
#> 154 C
#> 155 G
#> ref
#> 1 C
#> 2 C
#> 3 A
#> 4 G
#> 5 CTTTCTTTCTTTCTTTTTCTTT
#> 6 TTCTTTCTTTTTCTTTC
#> 7 TCTTTCTTTTTCTTTCTTC
#> 8 CTTTCTTTTTCTTT
#> 9 CTTTCTTTTTCTTT
#> 10 TTTCTTTCTTCCTTCCTTCCTTCCTTCCTTCCTCCCTTCCTTC
#> 11 G
#> 12 A
#> 13 C
#> 14 T
#> 15 T
#> 16 G
#> 17 C
#> 18 C
#> 19 C
#> 20 TG
#> 21 C
#> 22 C
#> 23 A
#> 24 A
#> 25 A
#> 26 C
#> 27 A
#> 28 T
#> 29 C
#> 30 T
#> 31 GGAAGGAAGGAAGGAAA
#> 32 C
#> 33 G
#> 34 GATTCCATTCGATGATTCCATTCA
#> 35 TTCCATTCGATGATTCCATTCAATTCCATTCGATGATGATTCCATTCGAG
#> 36 CCATTCGATGATTCCATTCAA
#> 37 TCCGCCGCCGCCGCGGCTTTTTGCCCCCCACCCCCGCCGCCGCGGCTTTTTACCCGCCGCGGCTTTTTGCCCCCCCGCCGCCGTGGTTTTTTCCCCCCATCTCACCTCCGCTTTTTGCCCGCCGCGGCTTTTTGCCCCCACCCCGCCTCGGCTTTTTGCCAGCCACGGCTTTTTGCCCCCCGCCACCGCGGCTTTTTGTCCC
#> 38 CGCCGCCGCCGCGGCTTTTTGCCCCCCACCCCCGCCGCCGCGGCTTTTTACCCGCCGCGGCTTTTTGCCCCCCCG
#> 39 GCCGCCGCCGCGGCTTTTTGCCCCCCACCCCCGCCGCCGCGGCTTTTTACCCGCCGCGGCTTTTTGCCCCCCCGCCGCCGTGGTTTTTTCCCCCCATCTCACCTCCGCTTTTTGCCCGCCGCGGCTTTTTGCCCCCACCCCGCCTCGGCTTTTTGCCAGCCACGGCTTTTTGCCCC
#> 40 T
#> 41 T
#> 42 A
#> 43 G
#> 44 A
#> 45 ACAGCCAGCCAGCCAAGCCAGCCAAGCCAGCCAGGAAAGCCAGCCTGCCAAGCCAGCCAAGCCAGCCAGCCACTCAAGCCAGCCAAGTCAGCGAGCCAACCAAGCCAGCCAACTCAGCCAGCCACCTAAGCCAGCCAAGCCAGCCAGCCAGCCAAGCAAGCCAGCCAGCCAAGCCAGCCAAGCCAGCCAAGCCAGGCAGCCAGCCAAGCCAGCCAAGCCAGCCAGCCAGCCAAGCCAGCCAGCCAGCCCACACAGCCAAGC
#> 46 TCAAGCCAGCCAAGTCAGCGAGCCAACCAAGCCAGCCAACTCAGCCAGCCACCTAAGCCAGCCAAGCCAGCCAGCCAGCCAAGCAAGCCAGCCAGCCAAGCCAGCCAAGCCAGCCAAGCCAGGCAGCCAGC
#> 47 ACAGCCAAGACAGCCAGCCAGCCACGCAAGCCAAGCCAGCCAGCCAGGCAAGCCAGGCATGCCAGCCAAGCCATCCAGCCAGCCAAGCCAGGCGGCCAGCCAAGCCAGCCAAGCCACCCGGCCAGCCAAGCCACCCAAGCCACCCGGCCAGCCAGGCATCCAAGCCAGCCAAGT
#> 48 CAAGCCAGCCAGCTAGCCAAGCCACCCAGCCAGCCAGCCAGCCAAACCAGCCAAGCCAGCCAGCCAGCCAGCCAAGCCAGCCAAGCAAGCCAGCCAGCCAGCCAAGCCACGCAAGCCAGCCAGCCAGCCATGCCAGCCA
#> 49 CAAAAAAAAAAAAAA
#> 50 TCA
#> 51 TCTCTCC
#> 52 CTCTCCCTCTCTCTCTCTCTCTCTCCCT
#> 53 TCTCCCTCTCTCTCTCTCTCTCTCC
#> 54 CTCCCTCTCTCTCTCTCTCTCTCCCT
#> 55 G
#> 56 G
#> 57 C
#> 58 C
#> 59 GAAAAAAA
#> 60 AG
#> 61 C
#> 62 CTT
#> 63 CTTT
#> 64 TACACACAC
#> 65 TACACACAC
#> 66 TACACACAC
#> 67 TACACACAC
#> 68 TACACACAC
#> 69 C
#> 70 C
#> 71 TAA
#> 72 TAA
#> 73 G
#> 74 AT
#> 75 AAAAC
#> 76 AAAC
#> 77 A
#> 78 C
#> 79 C
#> 80 G
#> 81 GT
#> 82 G
#> 83 C
#> 84 T
#> 85 TACACAC
#> 86 C
#> 87 T
#> 88 A
#> 89 GGTGT
#> 90 GGTGT
#> 91 GGTGT
#> 92 GGTGT
#> 93 G
#> 94 G
#> 95 C
#> 96 G
#> 97 TCCAGTAAGAATCCAGTTCTC
#> 98 TCA
#> 99 C
#> 100 GAAAAA
#> 101 GAAAAA
#> 102 G
#> 103 ATTTATT
#> 104 ATT
#> 105 T
#> 106 T
#> 107 CA
#> 108 CA
#> 109 CT
#> 110 A
#> 111 AT
#> 112 ATTTT
#> 113 G
#> 114 CTT
#> 115 A
#> 116 TCAAGACATCCTCCACAGAGGACC
#> 117 CAA
#> 118 CAA
#> 119 CTTT
#> 120 CTTT
#> 121 T
#> 122 C
#> 123 AGTTATGGAGGTTAGGGAGGTTAGGGAAGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTAGGGAG
#> 124 TTATGGAGGTTAGGGAGGTTAG
#> 125 TGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTAG
#> 126 GGAGGTTAGGGAGGTTAGGGAGGTTAT
#> 127 AGGTT
#> 128 GTTA
#> 129 TTAGG
#> 130 AGGGAGGTTAGGGAG
#> 131 G
#> 132 G
#> 133 TAA
#> 134 TAA
#> 135 ATTTTTTTTT
#> 136 ATTTTTTTTT
#> 137 ATTTTTTTTT
#> 138 C
#> 139 G
#> 140 A
#> 141 A
#> 142 ACCCACACACACC
#> 143 C
#> 144 TA
#> 145 G
#> 146 A
#> 147 A
#> 148 CA
#> 149 A
#> 150 T
#> 151 T
#> 152 C
#> 153 GTATACATAAGATATATTATATATAATATATTATATAAATGTATTATATATAACATATTATATATAATATATT
#> 154 T
#> 155 T
#>
#> attr(,"ldPanelsByRegion")$`/tmp/RtmpmBLZhq/pecotmr-ctwas-ld/2_chr22_2.ld`$variance
#> chr22:15574750:C:A
#> 0.15512823
#> chr22:15635104:C:A
#> 0.13875000
#> chr22:15689224:A:C
#> 0.49753766
#> chr22:15773180:G:A
#> 0.07986172
#> chr22:15837995:CTTTCTTTCTTTCTTTTTCTTT:CTTTTTCTTTCTTTCTTTTTCTTT
#> 0.07986172
#> chr22:15838001:TTCTTTCTTTTTCTTTC:TTTTCTTTTTCTTTC
#> 0.18000000
#> chr22:15838002:TCTTTCTTTTTCTTTCTTC:*
#> 0.18000000
#> chr22:15838003:CTTTCTTTTTCTTT:ATTTCTTTTTCTTT
#> 0.10986052
#> chr22:15838003:CTTTCTTTTTCTTT:CTTTTTCTTTTTCTTT
#> 0.16652832
#> chr22:15838010:TTTCTTTCTTCCTTCCTTCCTTCCTTCCTTCCTCCCTTCCTTC:TCTTCTTTCTTCCTTCCTTCCTTCCTTCCTTCCTCCCTTCCTTC
#> 0.19319392
#> chr22:15839920:G:A
#> 0.19319392
#> chr22:15919156:A:T
#> 0.42000000
#> chr22:15927084:C:T
#> 0.19319392
#> chr22:15947643:T:C
#> 0.10986052
#> chr22:15984722:T:C
#> 0.41319472
#> chr22:16073625:G:T
#> 0.19319392
#> chr22:16102937:C:T
#> 0.42652752
#> chr22:16111042:C:CA
#> 0.49875000
#> chr22:16112049:C:A
#> 0.45500000
#> chr22:16112091:TG:CG
#> 0.23111062
#> chr22:16115854:C:T
#> 0.49944442
#> chr22:16124912:C:T
#> 0.49652772
#> chr22:16132992:A:G
#> 0.49319452
#> chr22:16187126:A:G
#> 0.48875000
#> chr22:16207293:A:G
#> 0.36652812
#> chr22:16214693:C:A
#> 0.09500000
#> chr22:16217062:A:G
#> 0.49500000
#> chr22:16224528:T:C
#> 0.36652812
#> chr22:16234309:C:T
#> 0.49482917
#> chr22:16244919:T:C
#> 0.43277802
#> chr22:16254612:GGAAGGAAGGAAGGAAA:AGAAGGAAGGAAGGAAA
#> 0.14313283
#> chr22:16258960:C:A
#> 0.36652812
#> chr22:16262035:G:A
#> 0.36652812
#> chr22:16262334:GATTCCATTCGATGATTCCATTCA:G
#> 0.36652812
#> chr22:16262336:TTCCATTCGATGATTCCATTCAATTCCATTCGATGATGATTCCATTCGAG:*
#> 0.37500000
#> chr22:16262338:CCATTCGATGATTCCATTCAA:*
#> 0.36652812
#> chr22:16386749:TCCGCCGCCGCCGCGGCTTTTTGCCCCCCACCCCCGCCGCCGCGGCTTTTTACCCGCCGCGGCTTTTTGCCCCCCCGCCGCCGTGGTTTTTTCCCCCCATCTCACCTCCGCTTTTTGCCCGCCGCGGCTTTTTGCCCCCACCCCGCCTCGGCTTTTTGCCAGCCACGGCTTTTTGCCCCCCGCCACCGCGGCTTTTTGTCCC:*
#> 0.15755071
#> chr22:16386751:CGCCGCCGCCGCGGCTTTTTGCCCCCCACCCCCGCCGCCGCGGCTTTTTACCCGCCGCGGCTTTTTGCCCCCCCG:*
#> 0.11160580
#> chr22:16386752:GCCGCCGCCGCGGCTTTTTGCCCCCCACCCCCGCCGCCGCGGCTTTTTACCCGCCGCGGCTTTTTGCCCCCCCGCCGCCGTGGTTTTTTCCCCCCATCTCACCTCCGCTTTTTGCCCGCCGCGGCTTTTTGCCCCCACCCCGCCTCGGCTTTTTGCCAGCCACGGCTTTTTGCCCC:CCCGCCGCCGCGGCTTTTTGCCCCCCACCCCCGCCGCCGCGGCTTTTTACCCGCCGCGGCTTTTTGCCCCCCCGCCGCCGTGGTTTTTTCCCCCCATCTCACCTCCGCTTTTTGCCCGCCGCGGCTTTTTGCCCCCACCCCGCCTCGGCTTTTTGCCAGCCACGGCTTTTTGCCCC
#> 0.48513671
#> chr22:16400343:T:C
#> 0.21875000
#> chr22:16427771:T:C
#> 0.49875000
#> chr22:16439458:A:G
#> 0.23111062
#> chr22:16442170:G:A
#> 0.09500000
#> chr22:16549730:A:G
#> 0.10986052
#> chr22:16560460:ACAGCCAGCCAGCCAAGCCAGCCAAGCCAGCCAGGAAAGCCAGCCTGCCAAGCCAGCCAAGCCAGCCAGCCACTCAAGCCAGCCAAGTCAGCGAGCCAACCAAGCCAGCCAACTCAGCCAGCCACCTAAGCCAGCCAAGCCAGCCAGCCAGCCAAGCAAGCCAGCCAGCCAAGCCAGCCAAGCCAGCCAAGCCAGGCAGCCAGCCAAGCCAGCCAAGCCAGCCAGCCAGCCAAGCCAGCCAGCCAGCCCACACAGCCAAGC:*
#> 0.49482917
#> chr22:16560533:TCAAGCCAGCCAAGTCAGCGAGCCAACCAAGCCAGCCAACTCAGCCAGCCACCTAAGCCAGCCAAGCCAGCCAGCCAGCCAAGCAAGCCAGCCAGCCAAGCCAGCCAAGCCAGCCAAGCCAGGCAGCCAGC:CCAAGCCAGCCAAGTCAGCGAGCCAACCAAGCCAGCCAACTCAGCCAGCCACCTAAGCCAGCCAAGCCAGCCAGCCAGCCAAGCAAGCCAGCCAGCCAAGCCAGCCAAGCCAGCCAAGCCAGGCAGCCAGC
#> 0.09500000
#> chr22:16566547:ACAGCCAAGACAGCCAGCCAGCCACGCAAGCCAAGCCAGCCAGCCAGGCAAGCCAGGCATGCCAGCCAAGCCATCCAGCCAGCCAAGCCAGGCGGCCAGCCAAGCCAGCCAAGCCACCCGGCCAGCCAAGCCACCCAAGCCACCCGGCCAGCCAGGCATCCAAGCCAGCCAAGT:*
#> 0.25854588
#> chr22:16566742:CAAGCCAGCCAGCTAGCCAAGCCACCCAGCCAGCCAGCCAGCCAAACCAGCCAAGCCAGCCAGCCAGCCAGCCAAGCCAGCCAAGCAAGCCAGCCAGCCAGCCAAGCCACGCAAGCCAGCCAGCCAGCCATGCCAGCCA:TAAGCCAGCCAGCTAGCCAAGCCACCCAGCCAGCCAGCCAGCCAAACCAGCCAAGCCAGCCAGCCAGCCAGCCAAGCCAGCCAAGCAAGCCAGCCAGCCAGCCAAGCCACGCAAGCCAGCCAGCCAGCCATGCCAGCCA
#> 0.16652832
#> chr22:16841646:CAAAAAAAAAAAAAA:AAAAAAAAAAAAAAA
#> 0.07986172
#> chr22:16845585:TCA:TCACA
#> 0.36652812
#> chr22:16909478:TCTCTCC:*
#> 0.09652317
#> chr22:16909479:CTCTCCCTCTCTCTCTCTCTCTCTCCCT:CCCCTCTCTCTCTCTCTCTCTCCCT
#> 0.11160580
#> chr22:16909480:TCTCCCTCTCTCTCTCTCTCTCTCC:*
#> 0.09500000
#> chr22:16909481:CTCCCTCTCTCTCTCTCTCTCTCCCT:*
#> 0.09500000
#> chr22:16970638:G:A
#> 0.12444502
#> chr22:16973012:G:A
#> 0.13875000
#> chr22:17014255:C:T
#> 0.41319472
#> chr22:17051853:C:T
#> 0.33944482
#> chr22:17079499:GAAAAAAA:GAAAAAAAA
#> 0.38319412
#> chr22:17113082:AG:A
#> 0.10986052
#> chr22:17136539:C:T
#> 0.20206204
#> chr22:17154616:CTT:CTTT
#> 0.38319412
#> chr22:17154616:CTTT:CT
#> 0.15277722
#> chr22:17157085:TACACACAC:CACACACAC
#> 0.11160580
#> chr22:17157085:TACACACAC:T
#> 0.38738881
#> chr22:17157085:TACACACAC:TACACACACACACACAC
#> 0.43047951
#> chr22:17157085:TACACACAC:TACACACACACACACACACAC
#> 0.16906006
#> chr22:17157085:TACACACAC:TACACACACACACACACACACACAC
#> 0.14090747
#> chr22:17168884:C:T
#> 0.45500000
#> chr22:17172477:C:T
#> 0.37500000
#> chr22:17187665:TAA:TA
#> 0.13875000
#> chr22:17187665:TAA:TAAA
#> 0.37500000
#> chr22:17187977:G:GC
#> 0.16652832
#> chr22:17209889:AT:ATT
#> 0.20611162
#> chr22:17216769:AAAAC:ACAAAC
#> 0.13875000
#> chr22:17216770:AAAC:ACAAC
#> 0.18000000
#> chr22:17216771:A:AC
#> 0.22191952
#> chr22:17216771:C:A
#> 0.46322908
#> chr22:17216789:C:CACAT
#> 0.17436097
#> chr22:17216799:G:T
#> 0.16652832
#> chr22:17221295:GT:G
#> 0.37500000
#> chr22:17302680:G:A
#> 0.49652772
#> chr22:17303055:C:T
#> 0.49875000
#> chr22:17326841:T:C
#> 0.35777742
#> chr22:17327911:TACACAC:TACAC
#> 0.43277802
#> chr22:17331260:C:CT
#> 0.19319392
#> chr22:17350100:T:C
#> 0.49500000
#> chr22:17375405:A:G
#> 0.09500000
#> chr22:17379581:GGTGT:GGT
#> 0.10986052
#> chr22:17379581:GGTGT:GGTGTGT
#> 0.36652812
#> chr22:17379581:GGTGT:GGTGTGTGT
#> 0.28875000
#> chr22:17379581:GGTGT:GGTGTGTGTGT
#> 0.12444502
#> chr22:17427850:G:T
#> 0.49944442
#> chr22:17429117:G:A
#> 0.49986112
#> chr22:17449676:C:A
#> 0.25500000
#> chr22:17466675:G:T
#> 0.24319492
#> chr22:17469609:TCCAGTAAGAATCCAGTTCTC:TCAGTAAGAATCCAGTTCTC
#> 0.28875000
#> chr22:17469610:TCA:CCA
#> 0.47652792
#> chr22:17518422:C:T
#> 0.28875000
#> chr22:17523010:GAAAAA:AAAAAA
#> 0.18000000
#> chr22:17523010:GAAAAA:GA
#> 0.29944402
#> chr22:17577230:G:A
#> 0.09500000
#> chr22:17585626:ATTTATT:A
#> 0.25500000
#> chr22:17585630:ATT:*
#> 0.25500000
#> chr22:17658972:T:C
#> 0.17167130
#> chr22:17667743:T:A
#> 0.07986172
#> chr22:17683132:CA:C
#> 0.15277722
#> chr22:17683132:CA:CAAA
#> 0.29944402
#> chr22:17687818:CT:C
#> 0.37920110
#> chr22:17706998:A:G
#> 0.12444502
#> chr22:17721525:AT:ATTTTT
#> 0.12841938
#> chr22:17721525:ATTTT:AT
#> 0.37500000
#> chr22:17726847:G:A
#> 0.49500000
#> chr22:17734310:CTT:C
#> 0.29944402
#> chr22:17763207:A:G
#> 0.49875000
#> chr22:17765138:TCAAGACATCCTCCACAGAGGACC:T
#> 0.16652832
#> chr22:17768872:CAA:CA
#> 0.12841938
#> chr22:17768872:CAA:CAAA
#> 0.23781208
#> chr22:17839567:CTTT:CT
#> 0.37500000
#> chr22:17839567:CTTT:CTT
#> 0.09500000
#> chr22:17846396:T:TA
#> 0.32000000
#> chr22:17860245:C:A
#> 0.46444462
#> chr22:17876770:AGTTATGGAGGTTAGGGAGGTTAGGGAAGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTAGGGAG:GGTTATGGAGGTTAGGGAGGTTAGGGAAGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTAGGGAG
#> 0.08249026
#> chr22:17876799:TTATGGAGGTTAGGGAGGTTAG:*
#> 0.10986052
#> chr22:17876802:TGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTATGGAGGTTAGGGAGGTTAGGGAGGTTAG:*
#> 0.10986052
#> chr22:17876803:GGAGGTTAGGGAGGTTAGGGAGGTTAT:*
#> 0.13875000
#> chr22:17876805:AGGTT:*
#> 0.12444502
#> chr22:17876807:GTTA:*
#> 0.12444502
#> chr22:17876808:TTAGG:*
#> 0.12444502
#> chr22:17876810:AGGGAGGTTAGGGAG:*
#> 0.11160580
#> chr22:17879807:G:A
#> 0.13875000
#> chr22:17880174:G:A
#> 0.33944482
#> chr22:17898107:TAA:TA
#> 0.23111062
#> chr22:17898107:TAA:TAAA
#> 0.44444422
#> chr22:17929265:ATTTTTTTTT:ATTTTTT
#> 0.09500000
#> chr22:17929265:ATTTTTTTTT:ATTTTTTT
#> 0.38319412
#> chr22:17929265:ATTTTTTTTT:ATTTTTTTT
#> 0.49319452
#> chr22:17949102:C:T
#> 0.12444502
#> chr22:17955812:G:A
#> 0.32000000
#> chr22:17967486:A:ACACACACC
#> 0.26652732
#> chr22:17967486:A:ACACACC
#> 0.09500000
#> chr22:17967492:ACCCACACACACC:ACACACACACC
#> 0.32000000
#> chr22:17967494:C:*
#> 0.32000000
#> chr22:17977536:TA:TAA
#> 0.35777742
#> chr22:17998075:G:GTGAA
#> 0.35777742
#> chr22:18001877:A:C
#> 0.49652772
#> chr22:18064272:A:T
#> 0.30986152
#> chr22:18150441:CA:C
#> 0.23111062
#> chr22:18159414:A:G
#> 0.28875000
#> chr22:18160557:T:C
#> 0.34875000
#> chr22:18166484:T:TGA
#> 0.09500000
#> chr22:18173426:C:A
#> 0.23111062
#> chr22:18730960:GTATACATAAGATATATTATATATAATATATTATATAAATGTATTATATATAACATATTATATATAATATATT:*
#> 0.15755071
#> chr22:18731027:T:C
#> 0.08115506
#> chr22:18850784:T:G
#> 0.12444502
#>
#> attr(,"ldPanelsByRegion")$`/tmp/RtmpmBLZhq/pecotmr-ctwas-ld/2_chr22_2.ld`$sketch
#> class: RangedSummarizedExperiment
#> dim: 155 1000
#> metadata(2): genotypeSource ldProjection
#> assays(1): dosage
#> rownames(155): chr22:15574750:C:A chr22:15635104:C:A ...
#> chr22:18731027:T:C chr22:18850784:T:G
#> rowData names(4): SNP A1 A2 AF
#> colnames(1000): S1 S2 ... S999 S1000
#> colData names(0):
#>
#>
#>