R: Get gene names in each clusters and the expression profiling.

geneExpInCluster {cogena}

R Documentation

Get gene names in each clusters and the expression profiling.

Description

Get gene names in each clusters and the expression profiling. This output is helpful if user want to analyse the data for other application.

Usage

geneExpInCluster(object, method, nCluster)

## S4 method for signature 'cogena'
geneExpInCluster(object, method = clusterMethods(object),
  nCluster = nClusters(object))

Arguments

`object`	a genecl or cogena object
`method`	as clMethods in genecl function
`nCluster`	as nClust in cogena function.

Value

a list containing a matrix of cluster_id with expression profiling and label a vector of the sample labels.

Examples

data(Psoriasis)
annofile <- system.file("extdata", "c2.cp.kegg.v5.0.symbols.gmt.xz", 
package="cogena")

## Not run: 
genecl_result <- coExp(DEexprs, nClust=2:3, clMethods=c("hierarchical","kmeans"), 
    metric="correlation", method="complete", ncore=2, verbose=TRUE)

clen_res <- clEnrich(genecl_result, annofile=annofile, sampleLabel=sampleLabel)

#geneExpInCluster
geneExp <- geneExpInCluster(clen_res, "kmeans", "3")

## End(Not run)