mglR (version 0.1.0)

makePhenotypes: Make list of GWAS-based traits

Description

makePhenotypes returns a list with four elements summarizing the traits or phenotypes associated with each gene via GWAS results reported in both the GWAS catalog and GRASP. The first element (phenRes) is a list with length corresponding to the number of candidate genes and includes all GWAS-based phenotypes split by source: NHGRI-EBI GWAS Catalog and GRASP. The second element (phenList) collpases the first so only phenotypes for each gene are listed, regardless of the source. The third element (phenTable) is a dataframe with two columns: Phenotypes and gene names. The fourth element (phenCount) is a table with the number of elements corresponding to the number of unique phenotypes in the genelist - reported for each phenotype is the number of times it appears. It is sorted in descending order. The structure is similar to the makeGo and makeSnps functions.

Usage

makePhenotypes(mgl, saveFile = FALSE)

Arguments

mgl

List; see buildFromNames, buildFromRegion, or buildFromEnsgs

saveFile

A logical flag indicating whether a csv file ('Phenotypes.csv') should be saved in the current directory.

Details

This gives a summary of all traits associated with the gene in the NHGRI-EBI GWAS catalog and GRASP.

See Also

Other output: makeAeiPlot, makeCoXpGene, makeCoXpTranscript, makeDnaseSig, makeGoSearch, makeGo, makeMultiEqtl, makeOverlapTable, makeOverlap, makePhenotypeSearch, makeSnpSearch, makeSnps, makeSummary

Examples

exMgl() -> myMgl
myPhenotypes <- makePhenotypes(myMgl, saveFile = FALSE)