Hierarchical Multiple-Testing Correction for cis-QTL Association

Apply hierarchical (local per-gene + global across-gene) multiple-testing correction to a per-gene QtlSumStats of cis-QTL association statistics (one row per gene/trait), returning the same object enriched with the corrected-statistic columns. See qtlAssociationPostprocess.

Usage

qtlAssociationPostprocess(x, ...)

# S4 method for class 'QtlSumStats'
qtlAssociationPostprocess(
  x,
  fdrThreshold = 0.05,
  mafCutoff = 0,
  cisWindow = 0,
  methods = c("permutation", "bonferroni"),
  pvalueCol = "P",
  afCol = "af"
)

Arguments

x

A QtlSumStats.

...

Correction arguments.

fdrThreshold

Event- and variant-level FDR threshold (default 0.05).

mafCutoff

Minor-allele-frequency cutoff for the FILTERED Bonferroni flavour (fold of the per-variant af mcol). 0 disables it.

cisWindow

cis-window (bp) for the FILTERED Bonferroni flavour, applied to the per-variant tss_distance/tes_distance mcols. 0 disables it. When either mafCutoff or cisWindow is > 0 the *_filtered columns are produced (requires the n_variants_filtered row column).

methods

Correction families to compute: any of "permutation" (needs p_beta/beta_shape1/beta_shape2) and "bonferroni" (needs n_variants). The q-value SNP method adds no stored column – it is a significance query (see getSignificantQtls).

pvalueCol, afCol

Entry mcol names for the per-variant p-value / allele frequency (defaults "P" / "af").

Value

The input QtlSumStats with added correction columns.