padjust_genesets {goat}

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