mergeLists-methods: Function 'mergeLists' in Package 'categoryCompare'

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

Description

Merges the gene lists or the data tables from a ccGeneList object, providing a single table with all the input data, that can then be queried later, using cytTableOut

Usage

mergeLists(ccGeneList,ccOptions,isGene=TRUE)

Arguments

ccGeneList	a ccGeneList object
ccOptions	a ccOptions object
isGene	are the identifiers genes, or something else (metabolites, etc)

Value

A mergedData object which is really just a glorified data frame. If the ccGeneList input had a data list, then these are all merged into a single table. Otherwise, it contains just the gene names and which list they were present in.

Methods

signature(ccGeneList = "ccGeneList", ccOptions = "ccOptions")

See Also

ccGeneList ccOptions mergedData

Examples

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", data=table10[1:100,])
list48 <- list(genes=g48, universe=gUniverse, annotation="org.Hs.eg.db", data=table48[1:100,])

geneLists <- list(T10=list10, T48=list48)
geneLists <- new("ccGeneList", geneLists, ccType=c("BP","KEGG"))
ccOpts <- new("ccOptions", listNames = names(geneLists))
mergedDat <- mergeLists(geneLists,ccOpts)

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"))
ccOpts <- new("ccOptions", listNames = names(geneLists))
mergedDat <- mergeLists(geneLists,ccOpts)

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