geecc-package: Gene set enrichment for two or three categories

In geecc: Gene Set Enrichment Analysis Extended to Contingency Cubes

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 <[e-mail]>

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)

Example output

geecc
 1.10.0 loaded

Changed order of categories: deg,len,go
Testing: counts ~ deg + len + go (mi)

Dimension before filtering: deg=2, len=10, go=4
Dimension after filtering: deg=2, len=10, go=4

geecc documentation built on April 28, 2020, 8:19 p.m.