Master Gene List


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Documentation for package ‘mglR’ version 0.1.0

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addAei Add allele specific expression data to list
addAntisense Add antisense transcript information to list
addCisEqtl Add cis eQTL data to list
addDnase Add data from Maurano et. al. Nat Genet. 2015 regarding allele specific DNAse hypersensitivty.
addEnst Add transcript information to list
addExpression Add RNAsequencing expression data list
addGo Add gene ontology to list
addGrasp Add GWAS data from GRASP to list
addGwasCatalog Add GWAS data from NHGRI-EBI GWAS Catalog to list
addLoc Add gene location information to list
addPtv Add results from protein truncating variant algorithm made available by GTEx
addPubmed Adds number of titles from Pubmed to list
addSqtlAltrans Add results from Altrans splicingQTL algorithm to list
addSqtlSeek Add results from SqtlSeek splicingQTL algorithm to list
addTransEqtl Add trans eQTL data to list
buildFromEnsgs Build empty list using ENSG gene ids.
buildFromNames Build empty list using gene names.
buildFromRegion Build empty list using genomic region.
exampleMgl exampleMgl
exMgl exMgl
fixNames Fix genes with missing names
fixSnpIds Convert chr_pos to rs id
listElements Returns names of elements that are filled in
listSeparate Returns an individual element for each gene
makeAeiPlot Plot GTEx AEI ratios
makeCoXpGene Tests pairwise co-expression for normalized expression data
makeCoXpTranscript Tests pairwise co-expression between user defined transcripts in specified tissues
makeDnaseSig Filter Dnase (Maurano) Results
makeGo Returns a list with Gene Ontology data
makeGoSearch Returns gene names with a given GO term
makeMultiEqtl Returns SNPs identified as cis-eQTLs for more than one gene
makeOverlap Returns SNPs that appear in two user-defined groups for a given gene
makeOverlapTable Returns information for SNPs that appear in two user-defined groups for a given gene
makePhenotypes Make list of GWAS-based traits
makePhenotypeSearch Returns gene names with a given phenotype
makeSnps Make SNP list
makeSnpSearch Returns gene names with a given SNP
makeSummary Returns a summary table of the number of eQTL and GWAS SNPs for each gene
missNames Idenify genes with missing names