cogena_package {cogena} | R Documentation

## Co-expressed gene set enrichment analysis

### Description

To discovery smaller scale, but highly correlated cellular events that may be of great biological relevance, co-expressed gene set enrichment analysis, cogena, clusters gene expression profiles (coExp) and then make enrichment analysis for each clusters (clEnrich) based on hyper-geometric test. The heatmapCluster and heatmapPEI can visualise the results. See vignette for the detailed workflow.

### Source

https://github.com/zhilongjia/cogena

### Examples

    ## A quick start

    # Loading the examplar dataseat
    data(Psoriasis)

    # Clustering the gene expression profiling
    clMethods <- c("hierarchical","kmeans","diana","fanny","som","model","sota","pam","clara","agnes")
    genecl_result <- coExp(DEexprs, nClust=5:6, clMethods=clMethods,
        metric="correlation", method="complete", ncore=2, verbose=TRUE)

    # Gene set used
    annofile <- system.file("extdata", "c2.cp.kegg.v5.0.symbols.gmt.xz", package="cogena")

    # Enrichment analysis for clusters
    clen_res <- clEnrich(genecl_result, annofile=annofile, sampleLabel=sampleLabel)

    summary(clen_res)

    # Visualisation
    heatmapCluster(clen_res, "hierarchical", "6")
    heatmapPEI(clen_res, "hierarchical", "6", printGS=FALSE)

    # Obtain genes in a certain cluster
    head(geneInCluster(clen_res, "hierarchical", "6", "2"))

    ## The end

[Package cogena version 1.18.0 Index]