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mglR (version 0.1.0)
Master Gene List
Description
Tools to download and organize large-scale, publicly available genomic studies on a candidate gene scale. Includes functions to integrate these data sources and compare features across candidate genes.
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Version
Version
0.1.0
Install
install.packages('mglR')
Monthly Downloads
7
Version
0.1.0
License
GPL-3
Maintainer
Katherine Hartmann
Last Published
January 22nd, 2017
Functions in mglR (0.1.0)
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addGo
Add gene ontology to list
addCisEqtl
Add cis eQTL data to list
addGrasp
Add GWAS data from GRASP to list
addAei
Add allele specific expression data to list
addDnase
Add data from Maurano et. al. Nat Genet. 2015 regarding allele specific DNAse hypersensitivty.
addEnst
Add transcript information to list
addAntisense
Add antisense transcript information to list
addGwasCatalog
Add GWAS data from NHGRI-EBI GWAS Catalog to list
addExpression
Add RNAsequencing expression data list
addLoc
Add gene location information to list
buildFromNames
Build empty list using gene names.
addPubmed
Adds number of titles from Pubmed to list
addPtv
Add results from protein truncating variant algorithm made available by GTEx
buildFromRegion
Build empty list using genomic region.
addSqtlSeek
Add results from SqtlSeek splicingQTL algorithm to list
exMgl
exMgl
addSqtlAltrans
Add results from Altrans splicingQTL algorithm to list
exampleMgl
exampleMgl
addTransEqtl
Add trans eQTL data to list
buildFromEnsgs
Build empty list using ENSG gene ids.
fixSnpIds
Convert chr_pos to rs id
makeAeiPlot
Plot GTEx AEI ratios
makeGo
Returns a list with Gene Ontology data
listSeparate
Returns an individual element for each gene
makeDnaseSig
Filter Dnase (Maurano) Results
listElements
Returns names of elements that are filled in
makeCoXpGene
Tests pairwise co-expression for normalized expression data
makeGoSearch
Returns gene names with a given GO term
makeCoXpTranscript
Tests pairwise co-expression between user defined transcripts in specified tissues
fixNames
Fix genes with missing names
makePhenotypeSearch
Returns gene names with a given phenotype
makeOverlapTable
Returns information for SNPs that appear in two user-defined groups for a given gene
makeSummary
Returns a summary table of the number of eQTL and GWAS SNPs for each gene
makeSnps
Make SNP list
makePhenotypes
Make list of GWAS-based traits
missNames
Idenify genes with missing names
makeSnpSearch
Returns gene names with a given SNP
makeOverlap
Returns SNPs that appear in two user-defined groups for a given gene
makeMultiEqtl
Returns SNPs identified as cis-eQTLs for more than one gene