enrichOnto: enrichOnto

In ASPresearch/equivStandardTest: Implements a standard test of equivalence as described in (Sanchez et alt. 2019)

enrichOnto

Description

This function performs a standard test of equivalence between two gene lists

Usage

enrichOnto(
  geneList,
  geneUniverse,
  orgPackage = "org.Hs.eg.db",
  onto = c("BP", "MF", "CC"),
  pAdjustMeth = "BH",
  pvalCutoff = 0.01,
  qvalCutoff = 0.05
)

Arguments

geneList	character vector containing a FIRST gene list of entrez IDs
geneUniverse	character vector containing all genes from where geneLists have been extracted
orgPackage	A string wih the name of the annotation package
onto	string describing the ontology. Belongs to c('BP', 'MF', 'CC', 'ANY')
pAdjustMeth	string describing the adjust method. Belongs to c('BH', 'BY', 'Bonf')
pvalCutoff	A numeric value
qvalCutoff	A numeric value

Examples

 data(kidneyGeneLists)
 data(humanEntrezIDs)
 gl1 <-kidneyGeneLists[[1]]
 anOnto <- 'BP'
 enriched <- enrichOnto (geneL=gl1, geneUniverse=humanEntrezIDs, orgPackage='org.Hs.eg.db', onto=anOnto)
 GOIDs <- as.character(as.data.frame(enriched)$ID)

ASPresearch/equivStandardTest documentation built on March 28, 2022, 4:31 p.m.