testGeneFamilies.binomial {ShotgunFunctionalizeR}R Documentation

Identified significant gene families between two samples using the binomial model

Description

Test for significant gene families using the binomial model.

Usage

testGeneFamilies.binomial(data)

Arguments

data $2times n$ matrix containing counts

Details

testGeneFamilies.binomial performs an exact binomial test for each row in the data matrix. Assume that $X_1sim Po(M_1p_1)$ and $X_2sim Po(M_2p_2)$ where $M_1$ and $M_2$ are the total number of observations from two metagenomes. It follows that [ X_1|X_1+X_2=n sim Bin(n,frac{M_1p_1}{M_1p_1+M_2p_2}) ] and the binomial test is testing whether $p_1=p_2$. The test can be seen as an approximation of the hypergeometric counterpart (testGeneFamilies.hypergeometric).

testGeneFamilies.binomial is usually called implicitly by using the 'binomial' method in testGeneFamilies.

Value

testGeneFamilies.binomial returns a list with the following elements

PValues A list of p-values
Rankings.detail A list additional elements containing details about the ranking

See Also

testGeneFamilies, testGeneFamilies.hypergeometric, testGeneFamilies.gaussian, testGeneFamilies.poisson

Examples

counts<-cbind(rpois(10, 100), rpois(10, seq(50,300, length=10)))
testGeneFamilies.binomial(counts)

[Package ShotgunFunctionalizeR version 1.0-2 Index]