enrichment_in_groups: enrichment_in_groups

In biodataganache/leapR: Layered enrichment analysis of pathways R

enrichment_in_groups

Description

Calculate the enrichment in pathways using Fisher's exact or Kolgmorov-Smirnov test, using either the primary_columns to identify feature or the targets list. # access through leapr wrapper

Usage

enrichment_in_groups(
  geneset,
  targets = NULL,
  background = NULL,
  method = "fishers",
  minsize = 5,
  mapping_column = NULL,
  abundance_column = NULL,
  randomize = FALSE,
  silence_try_errors = TRUE
)

Arguments

geneset	geneset to use for enrichment
targets	targets to use for enrichmenet
background	'ExpressionSet' describing background to use
method	method to use for statistical test, options are 'fishers' or 'ks'
minsize	minimum size of set
mapping_column	column name of mapping identifiers
abundance_column	columns mapping abundance, either in the 'exprs' matrix or 'featureData'
randomize	true/false whether to randomize
silence_try_errors	true/false to silence errors

Value

data frame with enrichment results

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