sSeq-package {sSeq} | R Documentation

## Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size

### Description

This package is to discover the genes that differentially expressed between two conditions based on RNA-seq experiments. Gene expression is measured in counts of transcripts and modeled with the Negative Binomial (NB) distribution using a shrinkage approach for dispersion estimation. The method of moment (MM) estimates for dispersion are simply shrunk toward a target, which minimizes the average squared difference between the shrinkage estimates and the initial estimates. The exact per-gene probability under the NB model is calculated, and used to test the hypothesis that the expected expression of a gene in two conditions are not different.

### Details

Package: | sSeq
Type: | Package
Version: | 1.0
Date: | 2013-02-25

### Author(s)

Danni Yu <dyu@purdue.edu>, Wolfgang Huber <whuber@embl.de> and Olga Vitek <ovitek@purdue.edu>

### References

Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size

### Examples

    #load a simulated data that includes a count table
    data("countsTable")

    #calculate the p-values using the shrinkage approach.
    conds <- c("A", "B")
    resJS <- nbTestSH( countsTable, conds, "A", "B")

[Package sSeq version 1.28.0 Index]