geneSet-class: geneSet Class

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

Description

geneSet Class contains information for names of gene sets and a list of gene sets

Usage

numGene(x)

description(x)

geneSetList(x)

## S4 method for signature 'geneSet'
numGene(x)

## S4 method for signature 'geneSet'
description(x)

## S4 method for signature 'geneSet'
geneSetList(x)

Arguments

x	An geneSet object

Value

Object of class geneSet

Slots

numGene

numeric; the total number of all genes; This number is used in enrichment tests

description

vector of character; additional information for gene sets, such as names, URLs, a short description, etc.

geneSetList

list; a list of gene sets; each member is a vector containing a group of gene identifiers

Examples

biocarta.link.file <- system.file("extdata", 
    "geneSet/biocarta.txt", package="loci2path")
biocarta.link <- read.delim(biocarta.link.file, header=FALSE, 
    stringsAsFactors=FALSE)
biocarta.set.file <- system.file("extdata", "geneSet/biocarta.set.txt", 
    package="loci2path")
set.geneid <- read.table(biocarta.set.file, stringsAsFactors=FALSE)
set.geneid <- strsplit(set.geneid[,1], split=",")
names(set.geneid) <- biocarta.link[,1]
biocarta <- geneSet(
    geneSetList=set.geneid,
    description=biocarta.link[,2],
    numGene=31847)
numGene(biocarta)
head(description(biocarta))
head(geneSetList(biocarta))

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