R: "Correlates" a gene set collection with a given list of gene...

GSA.correlate {GSA} | R Documentation

## "Correlates" a gene set collection with a given list of gene nams

### Description

"Correlates" a gene set collection with a given list of gene names. Gives info on the overlap between the collection and the list of genes

### Usage

    GSA.correlate(GSA.genesets.obj, genenames)

### Arguments

`GSA.genesets.obj` | Gene set collection, created for example by GSA.read.gmt
`genenames` | Vector of gene names in expression daatset

### Details

Gives info on the overlap between a gene set collection and the list of gene names. This is for information purposes, to find out, for example, how many genes in the list of genes appear in the gene set collection.

### Author(s)

Robert Tibshirani

### References

Efron, B. and Tibshirani, R. On testing the significance of sets of genes. Stanford tech report rep 2006. http://www-stat.stanford.edu/~tibs/ftp/GSA.pdf

### Examples

    ######### two class unpaired comparison
    # y must take values 1,2

    set.seed(100)
    x<-matrix(rnorm(1000*20),ncol=20)
    dd<-sample(1:1000,size=100)

    u<-matrix(2*rnorm(100),ncol=10,nrow=100)
    x[dd,11:20]<-x[dd,11:20]+u
    y<-c(rep(1,10),rep(2,10))

    genenames=paste("g",1:1000,sep="")

    #create some random gene sets
    genesets=vector("list",50)
    for(i in 1:50){
     genesets[[i]]=paste("g",sample(1:1000,size=30),sep="")
    }
    geneset.names=paste("set",as.character(1:50),sep="")

    GSA.correlate(genesets, genenames)

[Package GSA version 1.03 Index]