eqtlSet-class: eqtlSet Class

Description Usage Arguments Value Slots Examples

Description

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

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
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/loci2path documentation built on Sept. 11, 2019, 8:21 a.m.