mglR (version 0.1.0)

makeGo: Returns a list with Gene Ontology data

Description

makeGo returns a list with three elements summarizing Gene Ontology (GO) terms. The first element (goRes) is the GO results subsetted from the mgl. The second element (goTable) is a dataframe with two columns: GO terms and gene names. The third element (goCount) is a table with the number of elements corresponding to the number of unique GO terms in the genelist - reported for each GO term is the number of times it appears. It is sorted in descending order.The structure is similar to the makePhenotypes and makeSnps functions.

Usage

makeGo(mgl, saveFile = TRUE)

Arguments

mgl

List; see buildFromNames, buildFromRegion, or buildFromEnsgs

saveFile

A logical flag indicating whether two csv files: 'GoTable.csv' and 'GoCount.csv' should be saved in the current directory

Details

Provides a brief summary of GO terms that have been associate with candidate genes. Of interest maybe groups of genes that have the same GO term see makeGoSearch.

See Also

Other output: makeAeiPlot, makeCoXpGene, makeCoXpTranscript, makeDnaseSig, makeGoSearch, makeMultiEqtl, makeOverlapTable, makeOverlap, makePhenotypeSearch, makePhenotypes, makeSnpSearch, makeSnps, makeSummary

Examples

exMgl() -> myMgl
makeGo(myMgl, saveFile = TRUE) -> myGo