makeOverlapTable: Returns information for SNPs that appear in two user-defined...
In mglR: Master Gene List

Description Usage Arguments Details See Also Examples

View source: R/makeOverlapTable_function.R

makeSummary returns a nested list with a dataframe for each gene, snp, source combination (i.e. myOverlapTable[[gene]][[snp]][[source]]).

1	makeOverlapTable(mgl, overlap, saveFile = TRUE)

`mgl`	List; see `buildFromNames`, `buildFromRegion`, or `buildFromEnsgs`
`overlap`	A list of overlapping snps made using `makeOverlap`
`saveFile`	A logical flag indicating whether a csv ('Overlap[groups].csv') should be saved in the current directory

For every gene with SNPs that overlap between two different user defined groups (see makeOverlap), provides a list of dataframes for each overlapping SNP that details the association whether it be eQTL, splicing, or trait-based. Provides the details for overlapping SNPs.

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

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exMgl() -> myMgl
makeOverlap(myMgl, snpsA = c('cisEqtls'), snpsB = c('gwasCatalog'), saveFile = TRUE) -> myOverlap
makeOverlapTable(myMgl, myOverlap, saveFile = TRUE) -> myOverlapTable