stdTest4GeneLists | R Documentation |
This function performs a "standard test" of equivalence between two gene lists
stdTest4GeneLists( genelist1, genelist2, geneUniverse, orgPackg, onto, GOLevel, restricted = FALSE, pAdjustMeth = "BH", pvalCutoff = 0.01, qvalCutoff = 0.05 )
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 |
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)
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