ccEnrich: Perform annotation enrichment for multiple gene lists

In categoryCompare: Meta-analysis of high-throughput experiments using feature annotations

Description

Takes a ccGeneList object containing all the information needed to perform enrichment calculations for Gene Ontology.

Usage

ccEnrich(ccGeneList)

Arguments

ccGeneList

A ccGeneList object, which is really just a list of lists, with some extra slots to tell us how to examine results. Each entry in the list should be named to allow identification later on. Each sub list should contain a vector genes denoting the genes of interest, a vector universe denoting the gene background (i.e. all genes on the chip), and an entry annotation denoting an organism database package (such as org.Hs.eg.db). See ccGeneList for more details regarding this object.

Details

This function is essentially a wrapper for hyperGTestCC that performs all of the calculations for the many gene lists in one go, returning a list of HyperGResultCC objects, one for each of the ccTypes and each gene list. These various HyperGResultCC objects can then be accessed and results compared among the lists for each of the ontologies

Value

A list of HyperGResultCC objects, one for each ccType and gene list, returned as ccEnrichResult objects for each ccType. This can be passed with a ccOptions object to ccCompare to generate actual annotation comparisons.

Author(s)

Robert M Flight

See Also

ccGeneList, hyperGTestCC, ccEnrichResult

Examples

## Not run: 
require(GO.db)
require(KEGG.db)
require(org.Hs.eg.db)

## End(Not run)
data(ccData)

g10 <- (unique(table10$Entrez[1:100]))
g48 <- (unique(table48$Entrez[1:100]))

list10 <- list(genes=g10, universe=gUniverse, annotation="org.Hs.eg.db")
list48 <- list(genes=g48, universe=gUniverse, annotation="org.Hs.eg.db")

geneLists <- list(T10=list10, T48=list48)
geneLists <- new("ccGeneList", geneLists, ccType=c("BP","KEGG"))
geneLists <- new("ccGeneList", geneLists, ccType=c("CC","KEGG"))

# set number of fdr runs to 0 to speed up runtime, not generally recommended.
geneLists <- new("ccGeneList", geneLists, ccType = c('BP','KEGG'), pvalueCutoff=0.01, fdr=0)
# enrichLists <- ccEnrich(geneLists)

categoryCompare documentation built on Nov. 8, 2020, 5:59 p.m.