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

Description Usage Arguments Value Examples

View source: R/analyze.R

Description

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

Usage

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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:

Examples

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

saeyslab/triwise documentation built on May 25, 2017, 11:31 p.m.