mergeLists-methods {categoryCompare} | R Documentation |
mergeLists
in Package categoryCompareMerges 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
mergeLists(ccGeneList,ccOptions,isGene=TRUE)
ccGeneList |
a |
ccOptions |
a |
isGene |
are the identifiers genes, or something else (metabolites, etc) |
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.
signature(ccGeneList = "ccGeneList", ccOptions = "ccOptions")
ccGeneList
ccOptions
mergedData
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)