p_values: Return a data.table with p-values of a tsum_exstra object.

In bahlolab/exSTRa: Expanded STR algorithm: detecting expansions in Illumina sequencing data

Return a data.table with p-values of a tsum_exstra object.

Description

Return a data.table with p-values of a tsum_exstra object.

Usage

p_values(
  tsum,
  correction = c("bf", "loci", "samples", "uncorrected"),
  alpha = 0.05,
  only.signif = FALSE,
  modify = FALSE,
  p.matrix = NULL
)

Arguments

tsum	An exstra_tsum object.
correction	Correction method to use. Use "bf" or TRUE for Bonferroni correction, and "uncorrected" or FALSE for no correction. ("bonferroni" is also acceptable). "samples" is Bonferroni correction by the number of tests (samples) at each locus. "loci" is Bonferroni correction by the number of loci.
alpha	Significance level alpha.
only.signif	If TRUE, only return significant results.
modify	If TRUE, will modify the tsum$stats table. Effectively ignored if only.sig == TRUE.
p.matrix	Matrix of p-values for internal use. Should only be used without tsum.

Value

A data.table keyed by "locus" then "sample". Other columns are tsum as calculated by tsum_test, p.value (uncorrected), signif (TRUE if significant after given correction), and p.value.sd, giving the standard deviation of the p-value estimate from the simulation.

bahlolab/exSTRa documentation built on Sept. 17, 2022, 5:08 p.m.