enrichment: get the enrichment table from a cogena object.

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

get the enrichment table from a cogena object.

Description

get the enrichment table from a cogena object with certain clustering methods and number of clusters.

Usage

enrichment(
  object,
  method,
  nCluster,
  CutoffNumGeneset = Inf,
  CutoffPVal = 0.05,
  orderMethod = "max",
  roundvalue = TRUE,
  add2 = FALSE
)

## S4 method for signature 'cogena'
enrichment(
  object,
  method,
  nCluster,
  CutoffNumGeneset = Inf,
  CutoffPVal = 0.05,
  orderMethod = "max",
  roundvalue = TRUE,
  add2 = TRUE
)

Arguments

object	a genecl or cogena object
method	as clMethods in genecl function
nCluster	as nClust in cogena function.
CutoffNumGeneset	the cut-off of the number of gene sets in the return table
CutoffPVal	the cut-off of p-value. The default is 0.05.
orderMethod	the order method, default is max, other options are "mean", "all", "I", "II" or a number meaning the ith cluster.
roundvalue	The default is TRUE. whether or not round the data. such as round(1.54, 1)=1.5
add2	enrichment score for add Up and Down reuglated genes.

Details

orderMethod:

• max. ordered by the max value in clusters beside all

• mean. ordered by the mean value in clusters beside all

• All. ordered by all genes

• I. ordered by the I cluster in two clusters (Up or Down-regulated, add2 should be TRUE)

• II. ordered by the II cluster in two clusters (Up or Down-regulated, add2 should be TRUE)

• a character number. like "3".

Value

a matrix with clusters in row and gene-sets in column.

Examples

data(Psoriasis)
annofile <- system.file("extdata", "c2.cp.kegg.v7.01.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)

enrichment.table1 <- enrichment(clen_res, "kmeans", "3")
enrichment.table2 <- enrichment(clen_res, "kmeans", "3", 
CutoffNumGeneset=10, orderMethod="mean")

## End(Not run)

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