geneToSNPList: Translate a List of Gene Ids to Their Corresponding SNP Ids

In cpvSNP: Gene set analysis methods for SNP association p-values that lie in genes in given gene sets

Description

Translates a set of gene ids to their corresponding SNPs.

Usage

geneToSNPList(geneList, arrayData, genes, maxgap = 20000, quiet = TRUE)

Arguments

geneList	An object of class GeneSetCollection or GeneSet where geneIds holds the gene Entrez ids.
arrayData	A GRanges object that corresponds to the probes for which data are present.
genes	A GRanges object holding the gene transcripts for which the mapping will occur. The ids of the genes should match the ids that are listed in the geneList object.
maxgap	An integer value indicating the flanking region around the gene for which SNPs are considered part of the gene. Default is 20000 (20kb).
quiet	A logical variable indicating whether warnings should be output from the SNP to gene mapping step.

Details

Translates a GeneSet or GeneSetCollection of gene Entrez ids to the corresponding SNPs that lie within a prespecified region of the gene.

Value

A GeneSetCollection object containing all SNP ids that lie within the genes listed in geneList.

Author(s)

Jason Hackney, Jessica Larson, Caitlin McHugh [e-mail]

Examples

    data(geneSetAnalysis)
    head(geneSetAnalysis$arrayData)
    arrayDataGR <- createArrayData(geneSetAnalysis[["arrayData"]], positionName="Position")
    
    library(TxDb.Hsapiens.UCSC.hg19.knownGene)
    genesHg19 <- genes(TxDb.Hsapiens.UCSC.hg19.knownGene)
	geneSets <- geneSetAnalysis[["geneSets"]]
	
	snpsGSC <- geneToSNPList(geneSets, arrayDataGR, genesHg19)

cpvSNP documentation built on Nov. 8, 2020, 6 p.m.