GOIDsInLevel: GOIDsInLevel

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

GOIDsInLevel

Description

This function extends getGOLevel returning only GO identifiers appearing between GO ancestors of at least one GeneList

Usage

GOIDsInLevel(
  GOLev,
  onto,
  geneList1 = NULL,
  geneList2 = NULL,
  orgPackage = NULL,
  restricted = TRUE
)

Arguments

GOLev	An integer
onto	string describing the ontology. Belongs to c('BP', 'MF', 'CC', 'ANY')
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

Examples

 data(kidneyGeneLists)
 GOLev <- 3
 anOnto <- 'BP'
 gl1 <- kidneyGeneLists[[1]]
 gl2 <- kidneyGeneLists[[2]]
 orgPkg ='org.Hs.eg.db'
 GOIDSinLevel.1 <- GOIDsInLevel (GOLev=GOLev, onto = anOnto,  restricted=FALSE); 
 length(GOIDSinLevel.1)
 GOIDSinLevel.2 <- GOIDsInLevel (GOLev=GOLev, onto = anOnto,  geneList1 = gl1, geneList2 = gl2, orgPackage =orgPkg)
 length(GOIDSinLevel.2)

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