GlobalAnalysis {GiANT}R Documentation

Global analyses

Description

Functions to perform global gene set analyses, as used in the globalStat parameter of gsAnalysis.

Usage

global.overrepresentation(dat,
	geneSet,
	coreSet)

global.ancova(dat,
	geneSet,
	labs,
	...)

global.test(dat,
	geneSet,
	labs,
	...)

Arguments

dat

A numeric matrix of gene expression values for all analyzed genes. Here, each row corresponds to one gene, and each column corresponds to one sample. The rows must be named with the gene names used in the gene sets.

geneSet

A gene set in form of a vector of gene names corresponding to the row names of dat.

coreSet

A gene set of interest resulting from an analysis of dat that should be compared to geneSet in the overrepresentation analysis. This is also a vector of gene names corresponding to the row names of dat.

labs

A vector of class labels for the samples in dat.

...

Further parameters for GlobalAncova and gt, as defined in the corresponding manual pages. The parameters xx, test.genes and group are set automatically by global.ancova, and the parameters alternative, subsets and response are set automatically by global.test.

Details

Wrapper functions for global gene set analyses.

Value

A list containing the following items:

pValue

The p-value for the significance of geneSet.

intersectGeneSetCoreSet

This element is only returned in case of an overrepresentation analysis and consists of a vector of genes included in both sets (geneSet and coreSet).

res.all

The full result object returned by fisher.test, GlobalAncova or gt respectively.

References

Hummel, M., Meister, R., Mansmann, U. (2008) GlobalANCOVA: exploration and assessment of gene group effects. Bioinformatics, 24(1), 78–85.

Goeman, J. J., van de Geer, S. A., de Kort, F., van Houwelingen, H. C. (2004) A global test for groups of genes: testing association with a clinical outcome. Bioinformatics, 20(1), 93–99.

See Also

geneSetAnalysis, gsAnalysis


[Package GiANT version 1.3.4 Index]