GPseq (version 0.5)

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

Description

Some functions for modeling sequence read counts as a generalized poisson model and to use this model for detecting differentially expressed genes in different conditions and differentially spliced exons.

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Version

Install

install.packages('GPseq')

Monthly Downloads

Version

0.5

License

GPL-2

Maintainer

Sudeep Srivastava

Last Published

July 6th, 2011

Functions in GPseq (0.5)

likelihood_ratio_poisson_exon_gene

Log Likelihood ratio statistic for comparison of the splicing ratio of an exon across two conditions using the Poisson Distribution

likelihood_ratio_tissue_generalized_poisson

Chi Square test statistic for comparison of expression levels of genes/exons across two conditions using the Generalized Poisson model

likelihood_ratio_generalized_poisson_exon_gene

Log Likelihood ratio statistic for comparison of the splicing ratio of an exon in two conditions

calc_chisq_statistic

Calculate Chi-square goodness of fit Statistic for Generalized Poisson and Poisson Models.

generalized_poisson_likelihood

Maximum Likelihood Estimates for the Generalized Poisson Model

estimate_differential_splicing

Estimating differential splicing statistics for an exon in a gene between all possible pairwise conditions

estimate_exon_gene_expression

Estimating Exon and Gene Expressions using the Poisson and Generalized Poisson Models and calculating their goodness of fit statistic

exons

Exon Annotation Database

genes

Gene annotations

estimate_differential_expression

Estimating differential expression statistics for Genes between all possible pairwise conditions

perform_permutation_ds

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

perform_permutation_de

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

reads

Mapped Reads

likelihood_ratio_tissue_poisson

Chi Square test statistic for comparison of expression levels of genes/exons across two conditions using the Poisson Model