enrichment_in_abundance: enrichment_in_abundance

In biodataganache/leapR: Layered enrichment analysis of pathways R

enrichment_in_abundance

Description

Enrichment in abundance calculates enrichment in pathways by the difference in abundance of the pathway members.

Usage

enrichment_in_abundance(
  geneset,
  eset,
  mapping_column = NULL,
  abundance_column = NULL,
  fdr = 0,
  matchset = NULL,
  sample_comparison = NULL,
  min_p_threshold = NULL,
  sample_n = NULL,
  silence_try_errors = TRUE
)

Arguments

geneset	Gene set to calculate enrichmnet
eset	Molecular abundance data in 'ExpressionSet' format
mapping_column	Column to use to map identifiers
abundance_column	Columns to use to quantify abundance
fdr	number of times to sample for FDR value
matchset	Name of a set to use for enrichment
sample_comparison	list of samples to use as comparison
min_p_threshold	Only include p-values lower than this
sample_n	size of sample to use
silence_try_errors	set to true to silence try errors

Value

data frame of enrichment result

biodataganache/leapR documentation built on July 16, 2025, 11:10 p.m.