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

In zhilongjia/cogena: co-expressed gene-set enrichment analysis

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.

See Also

clEnrich

Examples

data(Psoriasis)
annofile <- system.file("extdata", "c2.cp.kegg.v7.01.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)

zhilongjia/cogena documentation built on Nov. 21, 2023, 1:34 a.m.