Man pages for mglR
Master Gene List
| 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... |
| 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... |
| 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... |
| 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... |
| makeOverlapTable | Returns information for SNPs that appear in two user-defined... |
| 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... |
| missNames | Idenify genes with missing names |
