calc_chisq_statistic: Calculate Chi-square goodness of fit Statistic for...

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

Description

This function calculates the Chi-Square goodness of fit statistic for how well the input data fit a Generalized Poisson Model with given parameters theta and lambda and fit a Poisson Model with the MLE as the value for lambda.

Usage

calc_chisq_statistic(x, lambda, theta)

Arguments

x	This is the vector of observations or counts
lambda	This is lambda for the Generalized Poisson Model
theta	This is theta for the Generalized Poisson Model

Value

mark1	The Chi-Square test for the Generalized Poisson Model is valid only if mark1 = 1
mark2	The Chi-Square goodness of fit test for the Poisson model is valid only if mark2 = 1.
df1	Degrees of freedom for the chi-square statistic for the fit to the Generalized Poisson Model
df2	Degrees of freedom for the chi-square statistic for the fit to the Poisson Model
chisq1	Chi Square statistic for the fit to the Generalized Poisson Model
chisq2	Chi Square Statistic for the fit to the Poisson Model

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

y = rpois(100,10);

out = generalized_poisson_likelihood(y);

if(out$mark == 1)
{
  chisq_out = calc_chisq_statistic(y,out$lambda,out$theta);
}

#Check for Goodness of Fit of Generalized Poisson Model
if(chisq_out$mark1 == 1)
{
  cat("Degree of Freedom = ",chisq_out$df1," Chi Square Statistic = ",chisq_out$chisq1,"\n");
}
#Check for Goodness of FIt of Poisson Model
if(chisq_out$mark2 == 1)
{
  cat("Degree of Freedom = ",chisq_out$df2," Chi Square Statistic = ",chisq_out$chisq2,"\n");
}
 

Example output

Degree of Freedom =  6  Chi Square Statistic =  20.49612 
Degree of Freedom =  7  Chi Square Statistic =  21.36744 

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