mglR (version 0.1.0)

makeSummary: Returns a summary table of the number of eQTL and GWAS SNPs for each gene

Description

makeSummary returns a dataframe with the number of rows corresponding to the number of genes in the list and columns: gene, Number of eQTL SNPs, Number of GWAS Catalog SNPs, Number of GRASP SNPs.

Usage

makeSummary(mgl, saveFile = FALSE)

Arguments

mgl

Object of class 'mgl'; see buildFromNames, buildFromRegion, or buildFromEnsgs

saveFile

Logical flag indicating whether a csv ('Summary.csv') should be saved in the current directory

Details

Provides a brief summary of variants that have been associated with expression and clinical traits. Of interest maybe genes that have evidence of regulatory variants but have not yet been tied to a clinical phenotype or those genes that have evidence of a clinical phenotype but have not yet been shown to have regulatory variants

See Also

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

Examples

exMgl() -> myMgl
makeSummary(myMgl, saveFile = TRUE)