tweeDEseq (version 1.18.0)

testShapePT: Test shape parameter of PT

Description

Function to test whether the shape parameter is equal to a given value.

Usage

testShapePT(x, a = 0)

Arguments

x

object of class 'mlePT'.

a

numeric scalar smaller than 1. The function will test whether the shape parameter is equal to the introduced 'a' (default is 0).

Value

numeric p-value of the test.

Details

By default a = 0, and therefore the function tests whether the count data follows a Negative-Binomial distribution or not. In this case, a Likelihood Ratio Test is performed. When the given value for 'a' is different from 0, a Wald test is performed.

If a = 1, the function tests whether the count data follows a Poisson distribution or not.

If a = 0.5, the function tests whether the count data follows a Poisson-inverse Gaussian distribution or not.

If a = -1, the function tests whether the count data follows a Polya-Aeppli distribution or not.

References

Esnaola M, Puig P, Gonzalez D, Castelo R and Gonzalez JR (2013). A flexible count data model to fit the wide diversity of expression profiles arising from extensively replicated RNA-seq experiments. BMC Bioinformatics 14: 254

A.H. El-Shaarawi, R. Zhu, H. Joe (2010). Modelling species abundance using the Poisson-Tweedie family. Environmetrics 22, pages 152-164. P. Hougaard, M.L. Ting Lee, and G.A. Whitmore (1997). Analysis of overdispersed count data by mixtures of poisson variables and poisson processes. Biometrics 53, pages 1225-1238.

See Also

gofTest mlePoissonTweedie compareCountDist

Examples

# Generate a random matrix of counts
counts <- rPT(n=1000, a=0.5, mu=10, D=5)

# Maximum likelihood estimation of the Poisson-Tweedie parameters
mleEstimate <- mlePoissonTweedie(x = counts, a.ini = 0, D.ini
= 10)

# Test whether data comes from Negative-Binomial distribution
testShapePT(mleEstimate)

# Test whether data comes from Poisson-inverse Gaussian
testShapePT(mleEstimate, a = 0.5)