upDownGene {cogena} | R Documentation

## 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)

    ## 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.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)

[Package cogena version 1.14.0 Index]