geneInCluster {cogena} | R Documentation |
Get gene names in a certain cluster. This is helpful if user want to get the detail of a cluster.
geneInCluster(object, method, nCluster, ith) ## S4 method for signature 'cogena' geneInCluster(object, method = clusterMethods(object), nCluster = nClusters(object), ith)
object |
a cogena object |
method |
a clustering method |
nCluster |
cluster number |
ith |
the i-th cluster (should no more than nCluster) |
a character vector containing the gene names.
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) #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)