crossTabGOIDs4GeneLists: crossTab4GeneLists

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

crossTab4GeneLists

Description

This function builds a cross-tabulation of enriched and non-enriched GO terms from two gene lists

Usage

crossTabGOIDs4GeneLists(
  genelist1,
  genelist2,
  geneUniverse,
  orgPackg,
  onto,
  GOLev,
  restricted = FALSE,
  pAdjustMeth = "BH",
  pvalCutoff = 0.01,
  qvalCutoff = 0.05
)

Arguments

genelist1	character vector containing a FIRST gene list of entrez IDs
genelist2	character vector containing a SECOND gene list of entrez IDs
geneUniverse	character vector containing all genes from where geneLists have been extracted
orgPackg	A string wih the name of the annotation package
onto	string describing the ontology. Belongs to c('BP', 'MF', 'CC', 'ANY')
GOLev	An integer
restricted	Boolean variable to decide how tabulation of GOIDs 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.
pAdjustMeth	string describing the adjust method. Belongs to c('BH', 'BY', 'Bonf')
pvalCutoff	A numeric value
qvalCutoff	A numeric value

Value

a cross-tabulation of enriched and non-enriched GO terms from two gene lists

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