eqtlSet-class {loci2path} | R Documentation |
eqtlSet Class contains information for eqtl-gene association, gene identifier, position of SNPs, etc.
tissue(x) eqtlId(x) eqtlRange(x) eqtlGene(x) ## S4 method for signature 'eqtlSet' tissue(x) ## S4 method for signature 'eqtlSet' eqtlId(x) ## S4 method for signature 'eqtlSet' eqtlRange(x) ## S4 method for signature 'eqtlSet' eqtlGene(x)
x |
An eqtlSet object |
Object of class eqtlSet
tissue
character; name of the cell/tissue of the eQTL study
eqtlId
character; name of the SNPs
eqtlRange
GenomicRanges; position of the SNPs
gene
character; gene identifier
require(GenomicRanges) brain.file <- system.file("extdata", "eqtl/brain.gtex.txt", package="loci2path") tab <- read.table(brain.file, stringsAsFactors=FALSE, header=TRUE) eqtlRange <- GRanges(seqnames=Rle(tab$snp.chr), ranges=IRanges(start=tab$snp.pos, width=1)) brain.eset <- eqtlSet(tissue="brain", eqtlId=tab$snp.id, eqtlRange=eqtlRange, gene=as.character(tab$gene.entrez.id)) tissue(brain.eset) head(eqtlId(brain.eset)) eqtlRange(brain.eset) head(eqtlGene(brain.eset))