gset.data: a sample gene-set data

In AGDEX: Agreement of Differential Expression Analysis

Description

gset.data A gene-set data belongs to the GeneSetCollection class of GSEABase package.

Usage

data(gset.data)

Details

This sample gene-sets data contain 10 small gene-sets which are randomly selected from the full pathway gene-sets downloaded from http://www.broadinstitute.org/gsea/msigdb/download_file.jsp?filePath=/resources/msigdb/3.0/c5.all.v3.0.orig.gmt. The full gene-set data contain 1454 gene-sets. For the sample gene-set data of AGDEX package, 10 gene-sets are randomly selected, each has 20 to 30 probe-sets. Each gene-set has 20 to 30 probe-sets. We used getGmt function from GSEABase to read GMT format into a GeneSetCollection class object, then map the genes to probe-set IDs using hgu133 plus2 annotation data which contains the mapping from genes to probe-sets indentifiers.

See Also

GeneSetCollection-class

agdex; human.data; mouse.data; map.data

Examples

# download the pathway gene-sets data #
## Not run: 
 gset.url <- "http://www.broadinstitute.org/gsea/msigdb/download_file.jsp?filePath=/resources/msigdb/3.0/c5.all.v3.0.orig.gmt"
 gset.file.name <- unlist(strsplit(gset.url,split="/"))
 gset.file.name <- gset.file.name[length(gset.file.name)]
 gset.destination <- paste(local.data.dir,gset.file.name,sep="")
 download.file(gset.url, gset.destination)
 gset.file <- gset.destination
 gset.data <- getGmt(gset.file)        
 
# read in human U133+2 array annotation file#
 human.ann.data <- read.table("local human U133+2 array annotation data", head=T, sep="\t")
 genes.in.ann <- human.ann.data[,3]      # get the gene symbols from annotation file

# map the genes to probe-set IDs using human annotation data.########## 
 for (i in 1:length(gset.data))
  {
  genes.this.gset <- geneIds(gset.data[[i]])
  match.rows <- is.element(genes.in.ann, genes.this.gset) 
  probe.this.gset <- human.ann.data$ID[match.rows] 
  geneIds(gset.data[[i]]) <- as.character(probe.this.gset) 
  }

## End(Not run) 

AGDEX documentation built on Nov. 8, 2020, 8:32 p.m.