enrichment {cogena} | R Documentation

## 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.v5.0.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)

[Package cogena version 1.14.0 Index]