clEnrich_one: Gene set enrichment for clusters (for one clustering method...

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

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)

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