testEnrichment: Simple fisher's exact test for enrichment in a given set of...

In saeyslab/triwise: Gene expression changes in three biological conditions

Description

Simple fisher's exact test for enrichment in a given set of genes of interest (Goi)

Usage

testEnrichment(Goi, gsets, background, minknown = 2, mindiffexp = 2,
  maxknown = 500)

Arguments

Goi	character vector containing the genes tested for enrichment
gsets	List of character vectors, each containing a set of genes (gene identifiers)
background	character vector containing background gene identifiers
minknown	Minimal number of genes within a gene set for it to be considered for enrichment
mindiffexp	Minimal number of genes differentially expressed within a gene set for it to be considered for enrichment
maxknown	Maximal number of genes within a gene set for it to be considered for enrichment

Value

Dataframe containing for every gene set which passed the filtering:

• p-value of enrichment

• q-value of enrichment (p-value corrected for multiple testing)

• estimated odds score of enrichment, how much more likely is a given gene set to be part of

Examples

Goi = 1:50
gsets = list(a= 20:70, b = 45:80)
background = 1:100
testEnrichment(Goi, gsets, background)

saeyslab/triwise documentation built on May 29, 2019, 12:56 p.m.