testGeneFamilies {ShotgunFunctionalizeR}R Documentation

Tests for significant gene families

Description

Main test function

Usage

testGeneFamilies(data, method="Binomial", samples=c(1,2), 
                 multtest="BH", ord=TRUE, 
                 design.matrix=NULL, coef=1, 
                 covariates=NULL, log.covariates=FALSE, groups=NULL,
                 overdisp=FALSE)

Arguments

data A ShotgunFunctionalizeR data object (e.g. from readGeneFamilies)
method What statistical methods should be applied to the data?
samples Which samples should be compared? Only applicable for procedures comparing a pair of metagenomes (currently the binomial, hypergeometric and Gaussian procedure)
multtest What procedure should be used for correction for multiple testing. See mt.rawp2adjp in the multtest package for more information
ord Should the resulting ranking list be sorted?
design.matrix The design matrix. Only applicable when the general Poisson model is used
coef Which coefficient from the design matrix should be tested? Only applicable when the general Poisson model is used
covariates Covariates for poisson regression. Only applicable for regression analysis using the Poisson model
log.covariates Should the covariates be logged? Only applicable for regression analysis using the Poisson model
groups group labels for direct comparison. Only applicable for regression analysis using the Poisson model
overdisp Should the quasi-Poisson family with overdisperson be used for fitting the GLM? Only applicable when the Poisson model is used

See Also

readGeneFamilies, testGeneFamilies.binomial, testGeneFamilies.hypergeometric, testGeneFamilies.gaussian, testGeneFamilies.poisson, glm, family


[Package ShotgunFunctionalizeR version 1.0-2 Index]