filterGenesets: Filter a genesets results table

In sansomlab/gsfisher: Geneset Fisher

Filter a genesets results table

Description

Filter a genesets results table

Usage

filterGenesets(
  results_table,
  min_foreground_genes = 3,
  max_genes_geneset = 500,
  min_odds_ratio = 2,
  p_col = "p.val",
  padjust_method = "BH",
  use_adjusted_pvalues = TRUE,
  pvalue_threshold = 0.05
)

Arguments

results_table	A gofisher multi-sample results table.
min_foreground_genes	Minimum number of over-represent genes in foreground.
max_genes_geneset	Maximum number of genes in the full geneset (used to remove generic categories).
min_odds_ratio	Only genesets with odds ratios equal to or greater will be considered.
padjust_method	Correction method. Can be abbreviated (see p.adjust.methods).
pvalue_threshold	P-value threshold.
adjust_pvalues	Logical value indicating whether to adjust p-values across all sample.

Author(s)

Steve Sansom

sansomlab/gsfisher documentation built on July 7, 2022, 4:21 a.m.