crossTabGOIDs4GeneLists: crossTab4GeneLists

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

crossTab4GeneLists

Description

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

Usage

crossTabGOIDs4GeneLists(
  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
 crossTabFromGeneListsUnrestricted <- crossTabGOIDs4GeneLists (genelist1=gl1, genelist2=gl2,
 geneUniverse=humanEntrezIDs, orgPackg="org.Hs.eg.db", onto=anOnto, GOLevel=GOLev, restricted=restricted)
 restricted <- TRUE
 crossTabFromGeneListsRestricted <- crossTabGOIDs4GeneLists (genelist1=gl1, genelist2=gl2,
 geneUniverse=humanEntrezIDs, orgPackg="org.Hs.eg.db", onto=anOnto, GOLevel=GOLev, restricted=restricted)

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