upDownGene: Show up or down-regualted genes for a clustering method and...

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

Show up or down-regualted genes for a clustering method and the number of clusters.

Description

The value means up or down regulated genes for each cluster. 1 suggests that genes in the cluster is up-regualted genes, while -1 down-regualted genes. value within (-1, 1) means genes there are both up and down regulated genes in the cluster. Return a vector with the length of nCluster if add2 is FALSE, or the length of nCluster + 2 if add2 is TRUE and nCluster is not 2. In the latter situation, the last two itemes represent Up and Down reuglated genes

Usage

upDownGene(object, method, nCluster, add2 = FALSE)

## S4 method for signature 'cogena'
upDownGene(object, method, nCluster, add2 = FALSE)

logfc(dat, sampleLabel)

Arguments

object	a genecl or cogena object
method	as clMethods in genecl function
nCluster	cluster number
add2	add2 enrichment score for add Up and Down reuglated genes
dat	gene expression data frame
sampleLabel	factor. sampleLabel with names

Value

upDownGene: a vector

logfc: a data.frame

Examples

data(Psoriasis)
annofile <- system.file("extdata", "c2.cp.kegg.v7.01.symbols.gmt.xz", 
package="cogena")


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)

upDownGene(clen_res, "kmeans", "3", add2=TRUE)

upDownGene(clen_res, "kmeans", "2", add2=FALSE)

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