geneInCluster {cogena} | R Documentation

## Get gene names in a certain cluster.

### Description

Get gene names in a certain cluster. This is helpful if user want to get the detail of a cluster.

### Usage

    geneInCluster(object, method, nCluster, ith)

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

### Arguments

`object` | a cogena object
`method` | a clustering method
`nCluster` | cluster number
`ith` | the i-th cluster (should no more than nCluster)

### Value

a character vector containing the gene names.

### 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)

    #summay this cogena object
    summary(clen_res)

    #geneInCluster
    g1 <- geneInCluster(clen_res, "kmeans", "3", "2")

    #Up or Down genes with setting nCluster as "2".
    g2 <- geneInCluster(clen_res, "kmeans", "2", "1")

    ## End(Not run)

[Package cogena version 1.28.0 Index]