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.

### 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)

[Package cogena version 1.24.0 Index]