crossTabGOIDs: crossTabGOIDs

In pablof1988/goSorensen: Statistical inference based on the Sorensen-Dice dissimilarity and the Gene Ontology (GO)

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,
  GOLev,
  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')
GOLev	An integer
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
restricted	Boolean variable to decide how tabulation is performed. Unrestricted tabulation crosses _all_ GO Terms located at the level indicated by 'GOLev' with the two GOIDs lists Restricted tabulation crosses only terms from the selected GO level that are _common to ancestor terms of either list_. That is, if one term in the selected GO level is not an ancestor of at least one of the gene list most specific GO terms it is excluded from the GO Level's terms because it is impossible that it appears as being enriched.

Value

performs a crosstabulation between two lists of enriched GOTerms

pablof1988/goSorensen documentation built on July 21, 2023, 8:38 a.m.