makeSummary: Returns a summary table of the number of eQTL and GWAS SNPs...

In mglR: Master Gene List

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)

mglR documentation built on May 29, 2017, 4:07 p.m.