Example QTL Fine-Mapping Results with LBF (SuSiE)
Source:R/exampleData.R
qtlFineMappingLbfExample.RdA QtlFineMappingResult whose per-entry SuSiE fit
carries the full single-effect log-Bayes-factor matrix
(lbf_variable), posterior inclusion probabilities, and credible sets.
Unlike qtlFineMappingExample (a lightweight fit), this object
supports LBF-based downstream analysis such as colocPipeline.
Derived from the de-identified protocol_example toy data
(gene ENSG00000283047, chr22); all identifiers are synthetic.
Format
A QtlFineMappingResult with two rows (contexts
context1 and context2) for trait ENSG00000283047,
method susie. Each entry's susieFit carries
lbf_variable (single effects x variants), alpha, pip,
and credible-set membership.
Examples
data(qtlFineMappingLbfExample)
qtlFineMappingLbfExample
#> QtlFineMappingResult: 2 entries
#> 1 studies, 2 contexts, 1 traits, 1 methods
#> LD reference: NULL (individual-level fit)
head(topLoci(qtlFineMappingLbfExample))
#> GRanges object with 6 ranges and 31 metadata columns:
#> seqnames ranges strand | study context trait
#> <Rle> <IRanges> <Rle> | <character> <character> <character>
#> [1] chr22 10416669 * | test_study context1 ENSG00000283047
#> [2] chr22 10424460 * | test_study context1 ENSG00000283047
#> [3] chr22 10443846 * | test_study context1 ENSG00000283047
#> [4] chr22 10456378 * | test_study context1 ENSG00000283047
#> [5] chr22 10456420 * | test_study context1 ENSG00000283047
#> [6] chr22 10475014 * | test_study context1 ENSG00000283047
#> blockId method dataType dataSource standardized
#> <character> <character> <character> <character> <character>
#> [1] <NA> susie <NA> <NA> <NA>
#> [2] <NA> susie <NA> <NA> <NA>
#> [3] <NA> susie <NA> <NA> <NA>
#> [4] <NA> susie <NA> <NA> <NA>
#> [5] <NA> susie <NA> <NA> <NA>
#> [6] <NA> susie <NA> <NA> <NA>
#> variant_id chrom pos A1 A2
#> <character> <character> <integer> <character> <character>
#> [1] chr22:10416669:A:T chr22 10416669 T A
#> [2] chr22:10424460:A:T chr22 10424460 T A
#> [3] chr22:10443846:A:T chr22 10443846 T A
#> [4] chr22:10456378:A:T chr22 10456378 T A
#> [5] chr22:10456420:A:T chr22 10456420 T A
#> [6] chr22:10475014:A:T chr22 10475014 T A
#> N af posterior_effect posterior_se theta pip
#> <numeric> <numeric> <numeric> <numeric> <numeric> <numeric>
#> [1] 49 0.622449 0.00256440 0.0206322 NA 0.0310192
#> [2] 49 0.734694 0.00170607 0.0171620 NA 0.0260968
#> [3] 49 0.887755 0.00205156 0.0185858 NA 0.0280609
#> [4] 49 0.714286 -0.00154173 0.0164768 NA 0.0251818
#> [5] 49 0.551020 0.01785522 0.0574818 NA 0.1081658
#> [6] 49 0.673469 -0.00197516 0.0182738 NA 0.0276231
#> logBF cs_95 cs_70 cs_50 cs_95_purity cs_70_purity
#> <numeric> <character> <character> <character> <numeric> <numeric>
#> [1] 0.2451361 susie_0 susie_0 susie_0 0 0
#> [2] 0.0655952 susie_0 susie_0 susie_0 0 0
#> [3] 0.1400534 susie_0 susie_0 susie_0 0 0
#> [4] 0.0287607 susie_0 susie_0 susie_0 0 0
#> [5] 1.5685390 susie_0 susie_0 susie_0 0 0
#> [6] 0.1245209 susie_0 susie_0 susie_0 0 0
#> cs_50_purity within_cs_pip gene event grange_start
#> <numeric> <numeric> <character> <character> <integer>
#> [1] 0 NA <NA> <NA> <NA>
#> [2] 0 NA <NA> <NA> <NA>
#> [3] 0 NA <NA> <NA> <NA>
#> [4] 0 NA <NA> <NA> <NA>
#> [5] 0 NA <NA> <NA> <NA>
#> [6] 0 NA <NA> <NA> <NA>
#> grange_end
#> <integer>
#> [1] <NA>
#> [2] <NA>
#> [3] <NA>
#> [4] <NA>
#> [5] <NA>
#> [6] <NA>
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths