testGeneCategories {ShotgunFunctionalizeR}R Documentation

Tests for significant gene categories

Description

Main test function

Usage

testGeneCategories(data, method="GaussianSum", 
                   category="cogpathways", samples=c(1,2),
                   multtest="BH", ord=TRUE,
                   enrichment.method="Binomial",enrichment.p=0.1,
                   design.matrix=NULL, coef=1,             
                   covariates=NULL, log.covariates=FALSE, groups=NULL,
                   overdisp=FALSE)

Arguments

data Data object
method Method to use
category Which type of gene category should be used?
samples Samples to use
multtest Procedure for multiple testing correction
ord Should the resulting ranking list be sorted
enrichment.method Which method should be used for enrichment analysis
enrichment.p Which p-value cut-off should be used for enrichment analysis
design.matrix Design matrix for the general poisson model
coef Which coefficient from the design matrix should be used
covariates Covariates for poisson regression
log.covariates Should the covariates be logged?
groups Groups for direct comparison
overdisp Should the poisson model use overdispersion?

See Also

testGeneCategories.gaussiansum, testGeneCategories.independence, testGeneCategories.enrichment, testGeneCategories.poisson


[Package ShotgunFunctionalizeR version 1.0-3 Index]