stdTest4GeneLists: StandardTest4GeneLists

stdTest4GeneListsR Documentation

StandardTest4GeneLists

Description

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

Usage

stdTest4GeneLists(
  genelist1,
  genelist2,
  geneUniverse,
  orgPackg,
  onto,
  GOLevel,
  restricted = FALSE,
  pAdjustMeth = "BH",
  pvalCutoff = 0.01,
  qvalCutoff = 0.05
)

Arguments

geneUniverse

character vector containing all genes from where geneLists have been extracted

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

geneList1

character vector containing a FIRST gene list of entrez IDs

geneList2

character vector containing a SECOND gene list of entrez IDs

orgPackage

A string wih the name of the annotation package

GOLev

An integer

Examples

 data(kidneyGeneLists)
 data(humanEntrezIDs)
 gl1 <-kidneyGeneLists[[1]]
 gl2 <-kidneyGeneLists[[2]]
 anOnto <- 'BP'
 GOLev<- 3
 restricted = FALSE
 adjMeth<- 'BH'
 pValCut <- 0.05
 qValCut <- 0.01
 testedFromGeneLists <- stdTest4GeneLists (genelist1=gl1, genelist2=gl2,
 geneUniverse=humanEntrezIDs, orgPackg="org.Hs.eg.db", onto=anOnto, GOLevel=GOLev)


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