Extract Significant cis-QTL Variants

Derive the significant variants under a given correction method and FDR threshold from a QtlSumStats enriched by qtlAssociationPostprocess (significance is computed on demand, never stored).

Usage

getSignificantQtls(x, ...)

# S4 method for class 'QtlSumStats'
getSignificantQtls(
  x,
  method = c("permutation", "bonferroni_original", "bonferroni_filtered", "qvalue"),
  threshold = NULL
)

Arguments

x

A QtlSumStats.

...

Selection arguments (method, threshold).

method

Correction method whose significant variants to extract: "permutation", "bonferroni_original", "bonferroni_filtered", or "qvalue".

threshold

FDR threshold (defaults to the value stashed by qtlAssociationPostprocess).

Value

A GRanges (or list of GRanges) of the significant variants.

Examples

pBeta <- c(10^(-c(8, 7, 6, 5, 4, 3)), stats::ppoints(54))
G <- length(pBeta)
entries <- lapply(seq_len(G), function(i) {
  gr <- GenomicRanges::GRanges("chr1",
    IRanges::IRanges(seq(1000L, by = 50L, length.out = 4L), width = 1L))
  S4Vectors::mcols(gr) <- S4Vectors::DataFrame(
    SNP = paste0("g", i, "_v", 1:4), A1 = "A", A2 = "G",
    P = c(pBeta[i] / 5, 0.2, 0.5, 0.8),
    af = c(0.3, 0.2, 0.005, 0.4),
    tss_distance = c(0L, 500L, 900000L, 2000000L),
    tes_distance = c(0L, 500L, 900000L, 2000000L))
  gr
})
qss <- QtlSumStats(study = rep("s", G), context = rep("brain", G),
  trait = paste0("g", seq_len(G)), entry = entries, genome = "hg19",
  n_variants = rep(50L, G), n_variants_filtered = rep(30L, G),
  p_beta = pBeta, beta_shape1 = rep(1, G), beta_shape2 = rep(200, G))
pp <- qtlAssociationPostprocess(qss)
getSignificantQtls(pp)
#> GRanges object with 5 ranges and 10 metadata columns:
#>       seqnames    ranges strand |         SNP          A1          A2         P
#>          <Rle> <IRanges>  <Rle> | <character> <character> <character> <numeric>
#>   [1]     chr1      1000      * |       g1_v1           A           G     2e-09
#>   [2]     chr1      1000      * |       g2_v1           A           G     2e-08
#>   [3]     chr1      1000      * |       g3_v1           A           G     2e-07
#>   [4]     chr1      1000      * |       g4_v1           A           G     2e-06
#>   [5]     chr1      1000      * |       g5_v1           A           G     2e-05
#>              af tss_distance tes_distance       study     context       trait
#>       <numeric>    <integer>    <integer> <character> <character> <character>
#>   [1]       0.3            0            0           s       brain          g1
#>   [2]       0.3            0            0           s       brain          g2
#>   [3]       0.3            0            0           s       brain          g3
#>   [4]       0.3            0            0           s       brain          g4
#>   [5]       0.3            0            0           s       brain          g5
#>   -------
#>   seqinfo: 1 sequence from hg19 genome; no seqlengths