testGeneCategories {ShotgunFunctionalizeR} | R Documentation |
Main test function
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)
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? |
testGeneCategories.gaussiansum
,
testGeneCategories.independence
,
testGeneCategories.enrichment
,
testGeneCategories.poisson