mglR (version 0.1.0)

makeOverlapTable: Returns information for SNPs that appear in two user-defined groups for a given gene

Description

makeSummary returns a nested list with a dataframe for each gene, snp, source combination (i.e. myOverlapTable[[gene]][[snp]][[source]]).

Usage

makeOverlapTable(mgl, overlap, saveFile = TRUE)

Arguments

mgl

List; see buildFromNames, buildFromRegion, or buildFromEnsgs

overlap

A list of overlapping snps made using makeOverlap

saveFile

A logical flag indicating whether a csv ('Overlap[groups].csv') should be saved in the current directory

Details

For every gene with SNPs that overlap between two different user defined groups (see makeOverlap), provides a list of dataframes for each overlapping SNP that details the association whether it be eQTL, splicing, or trait-based. Provides the details for overlapping SNPs.

See Also

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

Examples

exMgl() -> myMgl
makeOverlap(myMgl, snpsA = c('cisEqtls'), snpsB = c('gwasCatalog'), saveFile = TRUE) -> myOverlap
makeOverlapTable(myMgl, myOverlap, saveFile = TRUE) -> myOverlapTable