geneInCluster: Get gene names in a certain cluster.

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

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)

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