GPseq (version 0.5)

perform_permutation_ds: Perform a Permutation Test to fit the null distribution of the test statistic to a Gamma Distribution

Description

This function calculates the shape and scale parameters for a Gamma Distribution which is used to fit the null distribution of the test statistic calculated for the Differential Splicing of an exon in a gene between two conditions/samples.

Usage

perform_permutation_ds(x,y,exon_start,exon_end,n,num_permute)

Arguments

x

Vector for counts of gene in sample 1

y

Vector for counts of gene in sample 2

exon_start

Start position of the exon in the gene

exon_end

End position of the exon in the gene

n

Length of the exon

num_permute

Number of times the permutation is done

Value

shape

The shape parameter of the Gamma distribution

scale

The scale parameter of the Gamma distribution

References

Consul, P. C. (1989) Generalized Poisson Distributions: Properties and Applications. New York: Marcel Dekker. Sudeep Srivastava, Liang Chen A two-parameter generalized Poisson model to improve the analysis of RNA-Seq data Nucleic Acids Research Advance Access published July 29,2010 doi : 10.1093/nar/gkq670

See Also

generalized_poisson_likelihood

Examples

x = rpois(100,10);
y = rpois(100,5);

exon_start = 1;
exon_end = 50;
gamma = perform_permutation_ds(x,y,exon_start,exon_end,50,60);

cat("Shape parameter = ",gamma$shape,"Scale parameter = ",gamma$scale);