ISACHR: Calculate chromosome enrichment for transcription modules

Description

Hypergeometric test(s) to check whether significantly many genes of an ISA module are on the same chromosome.

Usage

ISACHR (modules, ann = annotation(modules), features = featureNames(modules),  hgCutoff = 0.05, correction = TRUE, correction.method = "holm")

Arguments

modules

An ISAModules object, a set of ISA modules.

ann

Character scalar. The annotation package to be used. By default it is taken from the modules argument.

features

Character vector. The names of the features. By default it is taken from the modules argument.

hgCutoff

Numeric scalar. The cutoff value to be used for the enrichment significance. This can be changed later, without recalculating the test.

correction

Logical scalar, whether to perform multiple hypothesis testing correction.

correction.method

Character scalar, the multiple testing correction method to use. Possible values: “holm”, “hochberg”, “hommel”, “bonferroni”, “BH”, “BY”, “fdr”, “none”. See the p.adjust function for details on these.

Value

A CHRListHyperGResult object.

Details

The hypergeometric test, a version Fisher's exact test, takes a chromosome and a gene set (in our case coming from an ISA module) and asks whether the number of genes in the set that are on the given chromosome is significantly more (or less) than what one would expect by chance. ISACHR performs the hypergeometric test for every module, for every chromosome. The chromosome mapping is taken from the annotation package of the chip. ISACHR currently cannot test for under-representation.

References

Bergmann S, Ihmels J, Barkai N: Iterative signature algorithm for the analysis of large-scale gene expression data Phys Rev E Stat Nonlin Soft Matter Phys. 2003 Mar;67(3 Pt 1):031902. Epub 2003 Mar 11.

Examples

Run this code

data(ALLModulesSmall)
CHR <- ISACHR(ALLModulesSmall)
CHR
sigCategories(CHR)[[2]]
geneIdsByCategory(CHR)[[2]][[1]]

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