eqtlSet-class: eqtlSet Class

In StanleyXu/egquery: Loci2path: regulatory annotation of genomic intervals based on tissue-specific expression QTLs

Description

eqtlSet Class contains information for eqtl-gene association, gene identifier, position of SNPs, etc.

Usage

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)

Arguments

x	An eqtlSet object

Value

Object of class eqtlSet

Slots

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

Examples

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))

StanleyXu/egquery documentation built on Sept. 12, 2019, 9:35 a.m.