clEnrich_one {cogena} | R Documentation

## Gene set enrichment for clusters (for one clustering method and a certain number of clusters)

### Description

Gene set enrichment for clusters sourced from coExp function. the enrichment score are based on -log(p) with p from hyper-geometric test.

### Usage

    clEnrich_one(
      genecl_obj,
      method,
      nCluster,
      annofile = NULL,
      sampleLabel = NULL,
      TermFreq = 0
    )

### Arguments

`genecl_obj` | a genecl or cogena object
`method` | as clMethods in genecl function
`nCluster` | as nClust in cogena function
`annofile` | gene set annotation file
`sampleLabel` | sameple Label. Do make the label of interest located after the control label in the order of factor. See details.
`TermFreq` | a value from [0,1) to filter low-frequence gene sets

### Details

Gene sets availiable (See vignette for more):

- c2.cp.kegg.v7.01.symbols.gmt.xz (From Msigdb)

- c2.cp.reactome.v7.01.symbols.gmt.xz (From Msigdb)

- c5.bp.v7.01.symbols.gmt.xz (From Msigdb)

### Value

a list containing the enrichment score for each clustering methods and cluster numbers included in the genecl_obj

### Source

Gene sets are from

1. http://www.broadinstitute.org/gsea/msigdb/index.jsp

2. http://amp.pharm.mssm.edu/Enrichr/

### Examples

    #annotaion
    annoGMT <- "c2.cp.kegg.v7.01.symbols.gmt.xz"
    annofile <- system.file("extdata", annoGMT, package="cogena")

    data(Psoriasis)
    clMethods <- c("hierarchical","kmeans","diana","fanny","som","model","sota","pam","clara","agnes")
    genecl_result <- coExp(DEexprs, nClust=2:3, clMethods=c("hierarchical","kmeans"),
        metric="correlation", method="complete", ncore=2, verbose=TRUE)

    clen_res <- clEnrich_one(genecl_result, "kmeans", "3", annofile=annofile, sampleLabel=sampleLabel)
    clen_res1 <- clEnrich_one(clen_res, "hierarchical", "2", annofile=annofile, sampleLabel=sampleLabel)

[Package cogena version 1.28.0 Index]