Assemble cTWAS inputs from S4 GwasSumStats / TwasWeights
Source:R/ctwasPipeline.R
assembleCtwasInputs.RdBuilds the per-block ctwas-shape input set (z_snp,
weights, region_info, snp_map, LD_map, the LD-
and SNP-info loader closures, plus optional z_gene) that the
downstream ctwas steps consume. This is step 1 of the three-step
ctwasPipeline split.
Usage
assembleCtwasInputs(
gwasSumStats,
twasWeights,
twasZ = NULL,
fineMappingResult = NULL,
method = NULL,
twasWeightCutoff = 0,
csMinCor = 0.8,
minPipCutoff = 0,
maxNumVariants = Inf
)Arguments
- gwasSumStats
A
GwasSumStatswhose elements are LD blocks (at least two), keyed by itsblockIdcolumn, withgetQcInfo()non-empty. Build it withloadGwasSumStatsFromManifest(..., ldBlocks = <blocks>)and pass it throughsummaryStatsQc.- twasWeights
The per-gene weight source. Either (a) a FLAT
TwasWeights/QtlFineMappingResult(or a homogeneous list of them) carryingregionprovenance – each gene is placed into its home LD block internally bystart(region)(matching cTWAS'sp0assignment rule); or (b) a pre-bucketed NAMED LIST keyed byregion_id(keys a SUBSET ofgwasSumStats's), used as-is. Blocks without any TWAS weights still contribute their SNP-level signal to ctwas's joint group prior estimate (the legacy whole-chromosome pattern where only a few of many LD blocks carry gene weights). A gene whose cis span straddles a block boundary is homed by its single anchor; the cross-block signal is cTWAS's boundary-gene concern (mergeCtwasBoundaryRegions), not placement.- twasZ
Optional
GRangesof TWAS Z-scores (output ofcausalInferencePipeline). When supplied, the per-(trait, context) Z is used as thez_geneinput toctwas_sumstatsso it is not recomputed.- fineMappingResult
Optional
QtlFineMappingResultorGwasFineMappingResultcarrying the per-variant PIP and credible-set membership data used by the CS / PIP rescue filters (csMinCorandminPipCutoff). WhenNULL(default) the smart filters are no-ops; only the magnitude filter (twasWeightCutoff) and the per-gene cap (maxNumVariants, ordered by|weight|) apply.- method
Optional character (length 1). Picks which TWAS method's weights to feed into ctwas for each (study, context, trait) gene. When
NULL(default): use"ensemble"if that method is present across the weight sources; otherwise use the sole method when only one is present; otherwise run every method as an independent cTWAS run (oneCtwasResultrow-set per method). Passing the name explicitly (e.g."mrash") restricts the run to that single method.- twasWeightCutoff
Numeric (length 1). Drop variants with
|weight| < twasWeightCutofffrom each gene's weight matrix before ctwas sees it. Default0(no filter).- csMinCor
Numeric (length 1). When
fineMappingResultis provided, variants belonging to any 95% credible set with purity (min_abs_corr)>= csMinCorare marked as must-keep and survive the per-gene cap. Default0.8. Ignored without afineMappingResult.- minPipCutoff
Numeric (length 1). When
fineMappingResultis provided, variants with PIP greater thanminPipCutoffare marked as must-keep and survive the per-gene cap. Default0(no PIP rescue). Ignored without afineMappingResult.- maxNumVariants
Numeric (length 1). Cap on per-gene variant count. When the gene has more variants than this, keep all must-keep variants and fill remaining slots by descending PIP (when available) or descending
|weight|. DefaultInf(no cap).
Value
A list with elements z_snp, z_gene (NULL when no
twasZ), weights, region_info, snp_map,
LD_map, LD_loader_fun, snpinfo_loader_fun, and
resolvedMethod.
Details
The returned list is the SHARED STATE threaded through
estCtwasParam -> screenCtwasRegions ->
finemapCtwasRegions. Callers can short-circuit at any step
(e.g. override the estimated priors before fine-mapping) or call
ctwasPipeline() for the one-shot path.
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",
ldSketch = 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, 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
assembleCtwasInputs(gwasSumStats = gwasByRegion,
twasWeights = list(ctwasWeightsExample))
#> $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
#>
#> $z_gene
#> NULL
#>
#> $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`$R_wgt
#> chr22:10685239:C:T
#> chr22:10685239:C:T 1.000000000
#> chr22:10761227:G:A 0.523870971
#> chr22:11285239:C:T 0.129208067
#> chr22:11601805:G:A 0.089803623
#> chr22:11791698:G:T -0.126888645
#> chr22:11797697:C:T -0.100049383
#> chr22:12194389:G:A -0.145269377
#> chr22:12207043:C:T -0.058161912
#> chr22:12350816:G:A -0.134708464
#> chr22:12352464:C:A 0.003790412
#> chr22:12370627:C:T -0.293684481
#> chr22:12571373:AGAAAGAAAGAAAGAAAGAAG:* 0.026658676
#> chr22:12571377:AGAAAGAAAGAAAGAAG:* 0.040043562
#> chr22:12571385:AGAAAGAAG:* 0.066304610
#> chr22:12571386:GAAAGAAGGA:* 0.066304610
#> chr22:12571389:AGAAGGAAAGAAGGAAAGAAAGGAAGAAGGAAAGAAG:* 0.066304610
#> chr22:12576050:T:A 0.151977591
#> chr22:12640661:G:T -0.258330942
#> chr22:10761227:G:A
#> chr22:10685239:C:T 0.523870971
#> chr22:10761227:G:A 1.000000000
#> chr22:11285239:C:T 0.123137866
#> chr22:11601805:G:A 0.007146720
#> chr22:11791698:G:T -0.004667923
#> chr22:11797697:C:T -0.224936929
#> chr22:12194389:G:A -0.090839302
#> chr22:12207043:C:T 0.028848584
#> chr22:12350816:G:A -0.255319286
#> chr22:12352464:C:A 0.026428704
#> chr22:12370627:C:T -0.036246402
#> chr22:12571373:AGAAAGAAAGAAAGAAAGAAG:* 0.050967698
#> chr22:12571377:AGAAAGAAAGAAAGAAG:* 0.081623059
#> chr22:12571385:AGAAAGAAG:* 0.148282577
#> chr22:12571386:GAAAGAAGGA:* 0.148282577
#> chr22:12571389:AGAAGGAAAGAAGGAAAGAAAGGAAGAAGGAAAGAAG:* 0.148282577
#> chr22:12576050:T:A 0.284423199
#> chr22:12640661:G:T -0.166091729
#> chr22:11285239:C:T
#> chr22:10685239:C:T 0.12920807
#> chr22:10761227:G:A 0.12313787
#> chr22:11285239:C:T 1.00000000
#> chr22:11601805:G:A -0.01750337
#> chr22:11791698:G:T -0.05832883
#> chr22:11797697:C:T -0.15347765
#> chr22:12194389:G:A -0.13419119
#> chr22:12207043:C:T 0.22603533
#> chr22:12350816:G:A -0.14426316
#> chr22:12352464:C:A -0.16916073
#> chr22:12370627:C:T -0.06122762
#> chr22:12571373:AGAAAGAAAGAAAGAAAGAAG:* -0.03011705
#> chr22:12571377:AGAAAGAAAGAAAGAAG:* -0.01268563
#> chr22:12571385:AGAAAGAAG:* -0.09982767
#> chr22:12571386:GAAAGAAGGA:* -0.09982767
#> chr22:12571389:AGAAGGAAAGAAGGAAAGAAAGGAAGAAGGAAAGAAG:* -0.09982767
#> chr22:12576050:T:A 0.18340535
#> chr22:12640661:G:T -0.01574898
#> chr22:11601805:G:A
#> chr22:10685239:C:T 0.08980362
#> chr22:10761227:G:A 0.00714672
#> chr22:11285239:C:T -0.01750337
#> chr22:11601805:G:A 1.00000000
#> chr22:11791698:G:T 0.10102718
#> chr22:11797697:C:T 0.02761227
#> chr22:12194389:G:A -0.03598847
#> chr22:12207043:C:T 0.36222725
#> chr22:12350816:G:A 0.17848419
#> chr22:12352464:C:A -0.09401731
#> chr22:12370627:C:T -0.24732310
#> chr22:12571373:AGAAAGAAAGAAAGAAAGAAG:* -0.17074015
#> chr22:12571377:AGAAAGAAAGAAAGAAG:* -0.17402121
#> chr22:12571385:AGAAAGAAG:* -0.15385959
#> chr22:12571386:GAAAGAAGGA:* -0.15385959
#> chr22:12571389:AGAAGGAAAGAAGGAAAGAAAGGAAGAAGGAAAGAAG:* -0.15385959
#> chr22:12576050:T:A -0.16271808
#> chr22:12640661:G:T -0.22773619
#> chr22:11791698:G:T
#> chr22:10685239:C:T -0.126888645
#> chr22:10761227:G:A -0.004667923
#> chr22:11285239:C:T -0.058328829
#> chr22:11601805:G:A 0.101027178
#> chr22:11791698:G:T 1.000000000
#> chr22:11797697:C:T -0.114507716
#> chr22:12194389:G:A 0.065697688
#> chr22:12207043:C:T 0.205472685
#> chr22:12350816:G:A -0.118469220
#> chr22:12352464:C:A 0.053955885
#> chr22:12370627:C:T 0.086540193
#> chr22:12571373:AGAAAGAAAGAAAGAAAGAAG:* 0.096458266
#> chr22:12571377:AGAAAGAAAGAAAGAAG:* 0.115568791
#> chr22:12571385:AGAAAGAAG:* 0.154016463
#> chr22:12571386:GAAAGAAGGA:* 0.154016463
#> chr22:12571389:AGAAGGAAAGAAGGAAAGAAAGGAAGAAGGAAAGAAG:* 0.154016463
#> chr22:12576050:T:A -0.065586374
#> chr22:12640661:G:T 0.006669406
#> chr22:11797697:C:T
#> chr22:10685239:C:T -0.10004938
#> chr22:10761227:G:A -0.22493693
#> chr22:11285239:C:T -0.15347765
#> chr22:11601805:G:A 0.02761227
#> chr22:11791698:G:T -0.11450772
#> chr22:11797697:C:T 1.00000000
#> chr22:12194389:G:A 0.35136104
#> chr22:12207043:C:T -0.10424420
#> chr22:12350816:G:A 0.05220233
#> chr22:12352464:C:A -0.09506176
#> chr22:12370627:C:T 0.08340979
#> chr22:12571373:AGAAAGAAAGAAAGAAAGAAG:* -0.15067858
#> chr22:12571377:AGAAAGAAAGAAAGAAG:* -0.14337982
#> chr22:12571385:AGAAAGAAG:* -0.13489865
#> chr22:12571386:GAAAGAAGGA:* -0.13489865
#> chr22:12571389:AGAAGGAAAGAAGGAAAGAAAGGAAGAAGGAAAGAAG:* -0.13489865
#> chr22:12576050:T:A -0.16529364
#> chr22:12640661:G:T 0.13353653
#> chr22:12194389:G:A
#> chr22:10685239:C:T -0.14526938
#> chr22:10761227:G:A -0.09083930
#> chr22:11285239:C:T -0.13419119
#> chr22:11601805:G:A -0.03598847
#> chr22:11791698:G:T 0.06569769
#> chr22:11797697:C:T 0.35136104
#> chr22:12194389:G:A 1.00000000
#> chr22:12207043:C:T -0.11756369
#> chr22:12350816:G:A -0.14758477
#> chr22:12352464:C:A 0.01428417
#> chr22:12370627:C:T 0.16977198
#> chr22:12571373:AGAAAGAAAGAAAGAAAGAAG:* -0.06212933
#> chr22:12571377:AGAAAGAAAGAAAGAAG:* -0.04351896
#> chr22:12571385:AGAAAGAAG:* -0.02487634
#> chr22:12571386:GAAAGAAGGA:* -0.02487634
#> chr22:12571389:AGAAGGAAAGAAGGAAAGAAAGGAAGAAGGAAAGAAG:* -0.02487634
#> chr22:12576050:T:A -0.04813459
#> chr22:12640661:G:T 0.08166290
#> chr22:12207043:C:T
#> chr22:10685239:C:T -0.05816191
#> chr22:10761227:G:A 0.02884858
#> chr22:11285239:C:T 0.22603533
#> chr22:11601805:G:A 0.36222725
#> chr22:11791698:G:T 0.20547269
#> chr22:11797697:C:T -0.10424420
#> chr22:12194389:G:A -0.11756369
#> chr22:12207043:C:T 1.00000000
#> chr22:12350816:G:A -0.10504419
#> chr22:12352464:C:A -0.01480643
#> chr22:12370627:C:T -0.05292622
#> chr22:12571373:AGAAAGAAAGAAAGAAAGAAG:* -0.05374898
#> chr22:12571377:AGAAAGAAAGAAAGAAG:* -0.04941408
#> chr22:12571385:AGAAAGAAG:* -0.16423645
#> chr22:12571386:GAAAGAAGGA:* -0.16423645
#> chr22:12571389:AGAAGGAAAGAAGGAAAGAAAGGAAGAAGGAAAGAAG:* -0.16423645
#> chr22:12576050:T:A -0.12734931
#> chr22:12640661:G:T -0.05134283
#> chr22:12350816:G:A
#> chr22:10685239:C:T -0.13470846
#> chr22:10761227:G:A -0.25531929
#> chr22:11285239:C:T -0.14426316
#> chr22:11601805:G:A 0.17848419
#> chr22:11791698:G:T -0.11846922
#> chr22:11797697:C:T 0.05220233
#> chr22:12194389:G:A -0.14758477
#> chr22:12207043:C:T -0.10504419
#> chr22:12350816:G:A 1.00000000
#> chr22:12352464:C:A 0.03873224
#> chr22:12370627:C:T 0.02147026
#> chr22:12571373:AGAAAGAAAGAAAGAAAGAAG:* -0.07741414
#> chr22:12571377:AGAAAGAAAGAAAGAAG:* -0.05642252
#> chr22:12571385:AGAAAGAAG:* -0.17257222
#> chr22:12571386:GAAAGAAGGA:* -0.17257222
#> chr22:12571389:AGAAGGAAAGAAGGAAAGAAAGGAAGAAGGAAAGAAG:* -0.17257222
#> chr22:12576050:T:A -0.04554669
#> chr22:12640661:G:T 0.08035299
#> chr22:12352464:C:A
#> chr22:10685239:C:T 0.003790412
#> chr22:10761227:G:A 0.026428704
#> chr22:11285239:C:T -0.169160735
#> chr22:11601805:G:A -0.094017309
#> chr22:11791698:G:T 0.053955885
#> chr22:11797697:C:T -0.095061757
#> chr22:12194389:G:A 0.014284167
#> chr22:12207043:C:T -0.014806428
#> chr22:12350816:G:A 0.038732238
#> chr22:12352464:C:A 1.000000000
#> chr22:12370627:C:T -0.062975509
#> chr22:12571373:AGAAAGAAAGAAAGAAAGAAG:* 0.041834565
#> chr22:12571377:AGAAAGAAAGAAAGAAG:* 0.076849781
#> chr22:12571385:AGAAAGAAG:* -0.014620856
#> chr22:12571386:GAAAGAAGGA:* -0.014620856
#> chr22:12571389:AGAAGGAAAGAAGGAAAGAAAGGAAGAAGGAAAGAAG:* -0.014620856
#> chr22:12576050:T:A 0.189219719
#> chr22:12640661:G:T -0.170220536
#> chr22:12370627:C:T
#> chr22:10685239:C:T -0.29368448
#> chr22:10761227:G:A -0.03624640
#> chr22:11285239:C:T -0.06122762
#> chr22:11601805:G:A -0.24732310
#> chr22:11791698:G:T 0.08654019
#> chr22:11797697:C:T 0.08340979
#> chr22:12194389:G:A 0.16977198
#> chr22:12207043:C:T -0.05292622
#> chr22:12350816:G:A 0.02147026
#> chr22:12352464:C:A -0.06297551
#> chr22:12370627:C:T 1.00000000
#> chr22:12571373:AGAAAGAAAGAAAGAAAGAAG:* -0.10219161
#> chr22:12571377:AGAAAGAAAGAAAGAAG:* -0.08043681
#> chr22:12571385:AGAAAGAAG:* -0.04013377
#> chr22:12571386:GAAAGAAGGA:* -0.04013377
#> chr22:12571389:AGAAGGAAAGAAGGAAAGAAAGGAAGAAGGAAAGAAG:* -0.04013377
#> chr22:12576050:T:A 0.31042358
#> chr22:12640661:G:T 0.86662903
#> chr22:12571373:AGAAAGAAAGAAAGAAAGAAG:*
#> chr22:10685239:C:T 0.02665868
#> chr22:10761227:G:A 0.05096770
#> chr22:11285239:C:T -0.03011705
#> chr22:11601805:G:A -0.17074015
#> chr22:11791698:G:T 0.09645827
#> chr22:11797697:C:T -0.15067858
#> chr22:12194389:G:A -0.06212933
#> chr22:12207043:C:T -0.05374898
#> chr22:12350816:G:A -0.07741414
#> chr22:12352464:C:A 0.04183457
#> chr22:12370627:C:T -0.10219161
#> chr22:12571373:AGAAAGAAAGAAAGAAAGAAG:* 1.00000000
#> chr22:12571377:AGAAAGAAAGAAAGAAG:* 0.95201828
#> chr22:12571385:AGAAAGAAG:* 0.84836834
#> chr22:12571386:GAAAGAAGGA:* 0.84836834
#> chr22:12571389:AGAAGGAAAGAAGGAAAGAAAGGAAGAAGGAAAGAAG:* 0.84836834
#> chr22:12576050:T:A -0.04265345
#> chr22:12640661:G:T -0.11370964
#> chr22:12571377:AGAAAGAAAGAAAGAAG:*
#> chr22:10685239:C:T 0.04004356
#> chr22:10761227:G:A 0.08162306
#> chr22:11285239:C:T -0.01268563
#> chr22:11601805:G:A -0.17402121
#> chr22:11791698:G:T 0.11556879
#> chr22:11797697:C:T -0.14337982
#> chr22:12194389:G:A -0.04351896
#> chr22:12207043:C:T -0.04941408
#> chr22:12350816:G:A -0.05642252
#> chr22:12352464:C:A 0.07684978
#> chr22:12370627:C:T -0.08043681
#> chr22:12571373:AGAAAGAAAGAAAGAAAGAAG:* 0.95201828
#> chr22:12571377:AGAAAGAAAGAAAGAAG:* 1.00000000
#> chr22:12571385:AGAAAGAAG:* 0.88821190
#> chr22:12571386:GAAAGAAGGA:* 0.88821190
#> chr22:12571389:AGAAGGAAAGAAGGAAAGAAAGGAAGAAGGAAAGAAG:* 0.88821190
#> chr22:12576050:T:A -0.10140658
#> chr22:12640661:G:T -0.10339807
#> chr22:12571385:AGAAAGAAG:*
#> chr22:10685239:C:T 0.06630461
#> chr22:10761227:G:A 0.14828258
#> chr22:11285239:C:T -0.09982767
#> chr22:11601805:G:A -0.15385959
#> chr22:11791698:G:T 0.15401646
#> chr22:11797697:C:T -0.13489865
#> chr22:12194389:G:A -0.02487634
#> chr22:12207043:C:T -0.16423645
#> chr22:12350816:G:A -0.17257222
#> chr22:12352464:C:A -0.01462086
#> chr22:12370627:C:T -0.04013377
#> chr22:12571373:AGAAAGAAAGAAAGAAAGAAG:* 0.84836834
#> chr22:12571377:AGAAAGAAAGAAAGAAG:* 0.88821190
#> chr22:12571385:AGAAAGAAG:* 1.00000000
#> chr22:12571386:GAAAGAAGGA:* 1.00000000
#> chr22:12571389:AGAAGGAAAGAAGGAAAGAAAGGAAGAAGGAAAGAAG:* 1.00000000
#> chr22:12576050:T:A -0.07919564
#> chr22:12640661:G:T -0.07672631
#> chr22:12571386:GAAAGAAGGA:*
#> chr22:10685239:C:T 0.06630461
#> chr22:10761227:G:A 0.14828258
#> chr22:11285239:C:T -0.09982767
#> chr22:11601805:G:A -0.15385959
#> chr22:11791698:G:T 0.15401646
#> chr22:11797697:C:T -0.13489865
#> chr22:12194389:G:A -0.02487634
#> chr22:12207043:C:T -0.16423645
#> chr22:12350816:G:A -0.17257222
#> chr22:12352464:C:A -0.01462086
#> chr22:12370627:C:T -0.04013377
#> chr22:12571373:AGAAAGAAAGAAAGAAAGAAG:* 0.84836834
#> chr22:12571377:AGAAAGAAAGAAAGAAG:* 0.88821190
#> chr22:12571385:AGAAAGAAG:* 1.00000000
#> chr22:12571386:GAAAGAAGGA:* 1.00000000
#> chr22:12571389:AGAAGGAAAGAAGGAAAGAAAGGAAGAAGGAAAGAAG:* 1.00000000
#> chr22:12576050:T:A -0.07919564
#> chr22:12640661:G:T -0.07672631
#> chr22:12571389:AGAAGGAAAGAAGGAAAGAAAGGAAGAAGGAAAGAAG:*
#> chr22:10685239:C:T 0.06630461
#> chr22:10761227:G:A 0.14828258
#> chr22:11285239:C:T -0.09982767
#> chr22:11601805:G:A -0.15385959
#> chr22:11791698:G:T 0.15401646
#> chr22:11797697:C:T -0.13489865
#> chr22:12194389:G:A -0.02487634
#> chr22:12207043:C:T -0.16423645
#> chr22:12350816:G:A -0.17257222
#> chr22:12352464:C:A -0.01462086
#> chr22:12370627:C:T -0.04013377
#> chr22:12571373:AGAAAGAAAGAAAGAAAGAAG:* 0.84836834
#> chr22:12571377:AGAAAGAAAGAAAGAAG:* 0.88821190
#> chr22:12571385:AGAAAGAAG:* 1.00000000
#> chr22:12571386:GAAAGAAGGA:* 1.00000000
#> chr22:12571389:AGAAGGAAAGAAGGAAAGAAAGGAAGAAGGAAAGAAG:* 1.00000000
#> chr22:12576050:T:A -0.07919564
#> chr22:12640661:G:T -0.07672631
#> chr22:12576050:T:A
#> chr22:10685239:C:T 0.15197759
#> chr22:10761227:G:A 0.28442320
#> chr22:11285239:C:T 0.18340535
#> chr22:11601805:G:A -0.16271808
#> chr22:11791698:G:T -0.06558637
#> chr22:11797697:C:T -0.16529364
#> chr22:12194389:G:A -0.04813459
#> chr22:12207043:C:T -0.12734931
#> chr22:12350816:G:A -0.04554669
#> chr22:12352464:C:A 0.18921972
#> chr22:12370627:C:T 0.31042358
#> chr22:12571373:AGAAAGAAAGAAAGAAAGAAG:* -0.04265345
#> chr22:12571377:AGAAAGAAAGAAAGAAG:* -0.10140658
#> chr22:12571385:AGAAAGAAG:* -0.07919564
#> chr22:12571386:GAAAGAAGGA:* -0.07919564
#> chr22:12571389:AGAAGGAAAGAAGGAAAGAAAGGAAGAAGGAAAGAAG:* -0.07919564
#> chr22:12576050:T:A 1.00000000
#> chr22:12640661:G:T 0.25477343
#> chr22:12640661:G:T
#> chr22:10685239:C:T -0.258330942
#> chr22:10761227:G:A -0.166091729
#> chr22:11285239:C:T -0.015748981
#> chr22:11601805:G:A -0.227736186
#> chr22:11791698:G:T 0.006669406
#> chr22:11797697:C:T 0.133536528
#> chr22:12194389:G:A 0.081662903
#> chr22:12207043:C:T -0.051342832
#> chr22:12350816:G:A 0.080352990
#> chr22:12352464:C:A -0.170220536
#> chr22:12370627:C:T 0.866629027
#> chr22:12571373:AGAAAGAAAGAAAGAAAGAAG:* -0.113709642
#> chr22:12571377:AGAAAGAAAGAAAGAAG:* -0.103398074
#> chr22:12571385:AGAAAGAAG:* -0.076726305
#> chr22:12571386:GAAAGAAGGA:* -0.076726305
#> chr22:12571389:AGAAGGAAAGAAGGAAAGAAAGGAAGAAGGAAAGAAG:* -0.076726305
#> chr22:12576050:T:A 0.254773428
#> chr22:12640661:G:T 1.000000000
#>
#> $weights$`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
#>
#>
#>
#> $region_info
#> region_id chrom start stop
#> 1 chr22_1 22 10685239 12640661
#> 2 chr22_2 22 15574750 18850784
#>
#> $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
#> 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
#> 156 22
#> 157 22
#> 158 22
#> 159 22
#> 160 22
#> 161 22
#> 162 22
#> 163 22
#> 164 22
#> 165 22
#> 166 22
#> 167 22
#> 168 22
#> 169 22
#> 170 22
#> 171 22
#> 172 22
#> 173 22
#> 174 22
#> 175 22
#> id
#> 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
#> pos
#> 21 15574750
#> 22 15635104
#> 23 15689224
#> 24 15773180
#> 25 15837995
#> 26 15838001
#> 27 15838002
#> 28 15838003
#> 29 15838003
#> 30 15838010
#> 31 15839920
#> 32 15919156
#> 33 15927084
#> 34 15947643
#> 35 15984722
#> 36 16073625
#> 37 16102937
#> 38 16111042
#> 39 16112049
#> 40 16112091
#> 41 16115854
#> 42 16124912
#> 43 16132992
#> 44 16187126
#> 45 16207293
#> 46 16214693
#> 47 16217062
#> 48 16224528
#> 49 16234309
#> 50 16244919
#> 51 16254612
#> 52 16258960
#> 53 16262035
#> 54 16262334
#> 55 16262336
#> 56 16262338
#> 57 16386749
#> 58 16386751
#> 59 16386752
#> 60 16400343
#> 61 16427771
#> 62 16439458
#> 63 16442170
#> 64 16549730
#> 65 16560460
#> 66 16560533
#> 67 16566547
#> 68 16566742
#> 69 16841646
#> 70 16845585
#> 71 16909478
#> 72 16909479
#> 73 16909480
#> 74 16909481
#> 75 16970638
#> 76 16973012
#> 77 17014255
#> 78 17051853
#> 79 17079499
#> 80 17113082
#> 81 17136539
#> 82 17154616
#> 83 17154616
#> 84 17157085
#> 85 17157085
#> 86 17157085
#> 87 17157085
#> 88 17157085
#> 89 17168884
#> 90 17172477
#> 91 17187665
#> 92 17187665
#> 93 17187977
#> 94 17209889
#> 95 17216769
#> 96 17216770
#> 97 17216771
#> 98 17216771
#> 99 17216789
#> 100 17216799
#> 101 17221295
#> 102 17302680
#> 103 17303055
#> 104 17326841
#> 105 17327911
#> 106 17331260
#> 107 17350100
#> 108 17375405
#> 109 17379581
#> 110 17379581
#> 111 17379581
#> 112 17379581
#> 113 17427850
#> 114 17429117
#> 115 17449676
#> 116 17466675
#> 117 17469609
#> 118 17469610
#> 119 17518422
#> 120 17523010
#> 121 17523010
#> 122 17577230
#> 123 17585626
#> 124 17585630
#> 125 17658972
#> 126 17667743
#> 127 17683132
#> 128 17683132
#> 129 17687818
#> 130 17706998
#> 131 17721525
#> 132 17721525
#> 133 17726847
#> 134 17734310
#> 135 17763207
#> 136 17765138
#> 137 17768872
#> 138 17768872
#> 139 17839567
#> 140 17839567
#> 141 17846396
#> 142 17860245
#> 143 17876770
#> 144 17876799
#> 145 17876802
#> 146 17876803
#> 147 17876805
#> 148 17876807
#> 149 17876808
#> 150 17876810
#> 151 17879807
#> 152 17880174
#> 153 17898107
#> 154 17898107
#> 155 17929265
#> 156 17929265
#> 157 17929265
#> 158 17949102
#> 159 17955812
#> 160 17967486
#> 161 17967486
#> 162 17967492
#> 163 17967494
#> 164 17977536
#> 165 17998075
#> 166 18001877
#> 167 18064272
#> 168 18150441
#> 169 18159414
#> 170 18160557
#> 171 18166484
#> 172 18173426
#> 173 18730960
#> 174 18731027
#> 175 18850784
#> alt
#> 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
#> ref
#> 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
#>
#>
#> $LD_map
#> region_id
#> 1 chr22_1
#> 2 chr22_2
#> LD_file
#> 1 /tmp/RtmppU8QTb/temp_libpath984aa04109/pecotmr/extdata/ld_reference/chr22/protocol_example.LD.chr22.pgen
#> 2 /tmp/RtmppU8QTb/temp_libpath984aa04109/pecotmr/extdata/ld_reference/chr22/protocol_example.LD.chr22.pgen
#> SNP_file
#> 1 /tmp/RtmppU8QTb/temp_libpath984aa04109/pecotmr/extdata/ld_reference/chr22/protocol_example.LD.chr22.pgen
#> 2 /tmp/RtmppU8QTb/temp_libpath984aa04109/pecotmr/extdata/ld_reference/chr22/protocol_example.LD.chr22.pgen
#>
#> $LD_loader_fun
#> function (LD_file, ...)
#> {
#> panel <- ldPanelsByRegion[[LD_file]]
#> if (is.null(panel)) {
#> msg <- glue("ctwasPipeline LD loader: no cached panel for ",
#> "LD_file = '{LD_file}'")
#> abort(msg)
#> }
#> panel$R
#> }
#> <bytecode: 0x56441c3e8e18>
#> <environment: 0x56441c3e8600>
#>
#> $snpinfo_loader_fun
#> function (LD_file, ...)
#> {
#> panel <- ldPanelsByRegion[[LD_file]]
#> if (is.null(panel)) {
#> msg <- glue("ctwasPipeline snpInfo loader: no cached panel for ",
#> "LD_file = '{LD_file}'")
#> abort(msg)
#> }
#> panel$snpInfo
#> }
#> <bytecode: 0x56441c3e76e8>
#> <environment: 0x56441c3ead00>
#>
#> $resolvedMethod
#> [1] "susie"
#>