geneToSNPList {cpvSNP} | R Documentation |
Translates a set of gene ids to their corresponding SNPs.
geneToSNPList(geneList, arrayData, genes, maxgap = 20000, quiet = TRUE)
geneList |
An object of class |
arrayData |
A |
genes |
A |
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. |
Translates a GeneSet or GeneSetCollection of gene Entrez ids to the corresponding SNPs that lie within a prespecified region of the gene.
A GeneSetCollection
object containing all SNP ids that
lie within the genes listed in geneList.
Jason Hackney, Jessica Larson, Caitlin McHugh mchughc@uw.edu
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)