clEnrich {cogena} | R Documentation

## Gene set enrichment for clusters

### Description

Gene set enrichment for clusters sourced from coExp function. the enrichment score are based on -log2(p) with p from hyper-geometric test.

### Usage

    clEnrich(genecl_obj, annofile = NULL, sampleLabel = NULL,
      TermFreq = 0, ncore = 1)

### Arguments

`genecl_obj` | a genecl object
`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
`ncore` | the number of cores used

### Details

sampleLable: Use factor(c("Normal", "Cancer", "Normal"), levels=c("Normal", "Cancer")), instead of factor(c("Normal", "Cancer","Normal")). This parameter will affect the direction of gene regulation in cogena.

Gene sets availiable (See vignette for more):

- c2.cp.kegg.v5.0.symbols.gmt.xz (From Msigdb)

- c2.cp.reactome.v5.0.symbols.gmt.xz (From Msigdb)

- c5.bp.v5.0.symbols.gmt.xz (From Msigdb)

- c2.cp.biocarta.v5.0.symbols.gmt.xz (From Msigdb)

- c2.all.v5.0.symbols.gmt.xz (From Msigdb)

- c2.cp.v5.0.symbols.gmt.xz (From Msigdb)

- c5.mf.v5.0.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.v5.0.symbols.gmt.xz"
    annofile <- system.file("extdata", annoGMT, package="cogena")

    utils::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(genecl_result, annofile=annofile, sampleLabel=sampleLabel)

[Package cogena version 1.21.0 Index]