Extract Significant cis-QTL Variants — getSignificantQtls • pecotmr

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.