| perform_permutation_ds {GPseq} | R Documentation |
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.
perform_permutation_ds(x,y,exon_start,exon_end,n,num_permute)
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 |
shape |
The shape parameter of the Gamma distribution |
scale |
The scale parameter of the Gamma distribution |
Sudeep Srivastava, Liang Chen
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
generalized_poisson_likelihood
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);