geneSet-class {loci2path} | R Documentation |
geneSet Class contains information for names of gene sets and a list of gene sets
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)
x |
An geneSet object |
Object of class geneSet
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
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))