Man pages for mglR
Master Gene List

addAeiAdd allele specific expression data to list
addAntisenseAdd antisense transcript information to list
addCisEqtlAdd cis eQTL data to list
addDnaseAdd data from Maurano et. al. Nat Genet. 2015 regarding...
addEnstAdd transcript information to list
addExpressionAdd RNAsequencing expression data list
addGoAdd gene ontology to list
addGraspAdd GWAS data from GRASP to list
addGwasCatalogAdd GWAS data from NHGRI-EBI GWAS Catalog to list
addLocAdd gene location information to list
addPtvAdd results from protein truncating variant algorithm made...
addPubmedAdds number of titles from Pubmed to list
addSqtlAltransAdd results from Altrans splicingQTL algorithm to list
addSqtlSeekAdd results from SqtlSeek splicingQTL algorithm to list
addTransEqtlAdd trans eQTL data to list
buildFromEnsgsBuild empty list using ENSG gene ids.
buildFromNamesBuild empty list using gene names.
buildFromRegionBuild empty list using genomic region.
fixNamesFix genes with missing names
fixSnpIdsConvert chr_pos to rs id
listElementsReturns names of elements that are filled in
listSeparateReturns an individual element for each gene
makeAeiPlotPlot GTEx AEI ratios
makeCoXpGeneTests pairwise co-expression for normalized expression data
makeCoXpTranscriptTests pairwise co-expression between user defined transcripts...
makeDnaseSigFilter Dnase (Maurano) Results
makeGoReturns a list with Gene Ontology data
makeGoSearchReturns gene names with a given GO term
makeMultiEqtlReturns SNPs identified as cis-eQTLs for more than one gene
makeOverlapReturns SNPs that appear in two user-defined groups for a...
makeOverlapTableReturns information for SNPs that appear in two user-defined...
makePhenotypesMake list of GWAS-based traits
makePhenotypeSearchReturns gene names with a given phenotype
makeSnpsMake SNP list
makeSnpSearchReturns gene names with a given SNP
makeSummaryReturns a summary table of the number of eQTL and GWAS SNPs...
missNamesIdenify genes with missing names
mglR documentation built on May 29, 2017, 4:07 p.m.