clEnrich_one: Gene set enrichment for clusters (for one clustering method...
In cogena: co-expressed gene-set enrichment analysis

Description Usage Arguments Details Value Source Examples

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

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

`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

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)

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

Gene sets are from

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

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

#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)