geecc-package {geecc} | R Documentation

## Gene set enrichment for two or three categories

### Description

This package performs gene set enrichment analyses considering two or three categories. Categories might be regulated genes, sequence length, GC content, GO terms, KEGG pathways and so on.

### Author(s)

Markus Boenn Maintainer: Markus Boenn <markus.boenn@ufz.de>

### Examples

    ##
    ## a completely artificial example run
    ## through the routines of the package
    ##
    R <- 500
    #generate R random gene-ids
    ID <- sapply(1:R, function(r){paste( sample(LETTERS, 10), collapse="" ) } )
    ID <- unique(ID)

    #assign artificial differentially expressed genes randomly
    category1 <- list( deg.smallFC=sample(ID, 100, rep=FALSE),
    	deg.hughFC=sample(ID, 100, rep=FALSE) )
    #assign artificial GO terms of genes randomly
    category2 <- list( go1=sample(ID, 50, replace=FALSE),
    	go2=sample(ID, 166, replace=FALSE),
    	go3=sample(ID, 74, replace=FALSE),
    	go4=sample(ID, 68, replace=FALSE) )
    #assign artificial sequence length of genes randomly
    LEN <- setNames(sample(seq(100, 1000, 100), length(ID), replace=TRUE), ID)
    category3 <- split( ID, f=factor(LEN, levels=seq(100, 1000, 100)) )
    CatList <- list(deg=category1, go=category2, len=category3)

    ConCubFilter.obj <- new("concubfilter", names=names(CatList))
    ConCub.obj <- new("concub", categories=CatList)
    ConCub.obj.2 <- runConCub( obj=ConCub.obj, filter=ConCubFilter.obj, nthreads=1 )
    ConCub.obj.3 <- filterConCub( obj=ConCub.obj.2, filter=ConCubFilter.obj )
    plotConCub( obj=ConCub.obj.3, filter=ConCubFilter.obj )
    x <- getTable(ConCub.obj.3)

[Package geecc version 1.20.0 Index]