cogena (version 1.6.2)

upDownGene: 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

logfc: add MeanA, MeanB and logFC to the dat

Usage

upDownGene(object, method, nCluster, add2 = FALSE)
"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 vectorlogfc: a data.frame

Examples

data(Psoriasis)
annofile <- system.file("extdata", "c2.cp.kegg.v5.0.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)