crossTabGOIDs: crossTabGOIDs

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

crossTabGOIDs

Description

This function performs a crosstabulation between two lists of enriched GOTerms The lists are intended to have been obtained from enrichment analyses performed on two gene lists

Usage

crossTabGOIDs(
  GO1,
  GO2,
  onto,
  GOLevel,
  listNames = NULL,
  geneList1 = NULL,
  geneList2 = NULL,
  orgPackage = NULL,
  restricted = FALSE
)

Arguments

GO1	character vector containing a FIRST list of GO identifiers
GO2	character vector containing a SECOND gene list GO identifiers
onto	string describing the ontology. Belongs to c('BP', 'MF', 'CC', 'ANY')
listNames	character vector with names of the genelists that generated the enriched GOIDs
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(kidneyEnrichedGOIDs)
 GOIDs1 <-kidneyEnrichedGOIDs[[1]]
 GOIDs2 <-kidneyEnrichedGOIDs[[2]]
 names4lists<- names(kidneyEnrichedGOIDs)[1:2]
 anOnto <- 'BP'
 GOLev <- 3
 gl1 <- kidneyGeneLists[[1]]
 gl2 <- kidneyGeneLists[[2]]
 orgPkg ='org.Hs.eg.db'
 restrictTab <- TRUE
 crossTabbedGOIdsRestricted <- crossTabGOIDs (GO1 = GOIDs1, GO2 = GOIDs2, onto = anOnto, 
 GOLevel =GOLev, listNames=names4lists, geneList1 = gl1, geneList2 = gl2, orgPackage =orgPkg, restricted = restrictTab)
 show(crossTabbedGOIdsRestricted)
 restrictTab <- FALSE
 crossTabbedGOIdsUnrestricted <- crossTabGOIDs (GO1 = GOIDs1, GO2 = GOIDs2, onto = anOnto, 
 GOLevel =GOLev, listNames=names4lists, geneList1 = gl1, geneList2 = gl2, orgPackage =orgPkg, restricted = restrictTab)
 show(crossTabbedGOIdsUnrestricted)

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