perform_permutation_ds: Perform a Permutation Test to fit the null distribution of...

In GPseq: gpseq: Using the generalized Poisson distribution to model sequence read counts from high throughput sequencing experiments

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

Author(s)

Sudeep Srivastava, Liang Chen

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);

GPseq documentation built on May 30, 2017, 3:11 a.m.