padjust_genesets: Adjust p-values for all genesets, grouped by 'source' then...

In goat: Gene Set Analysis Using the Gene Set Ordinal Association Test

Adjust p-values for all genesets, grouped by 'source' then adjust for the number of 'sources'

Description

Adjust p-values for all genesets, grouped by 'source' then adjust for the number of 'sources'

Usage

padjust_genesets(
  genesets,
  method = "BH",
  cutoff = 0.01,
  correct_sources = TRUE
)

Arguments

genesets	tibble with genesets, must contain column 'pvalue'
method	method for multiple testing correction, must be any of stats::p.adjust.methods, e.g. "BH" or "bonferroni"
cutoff	numeric cutoff value for adjusted p-value, signif column is set to TRUE for all values lesser-equals
correct_sources	apply Bonferroni adjustment to all p-values according to the number of geneset sources that were tested. Boolean parameter, set TRUE to enable (default) or FALSE to disable

Value

updated genesets table

goat documentation built on April 3, 2025, 6:05 p.m.