nbinomGLMTest {DESeq} | R Documentation

## Perform chi-squared tests comparing two sets of GLM fits

### Description

For each gene, the function calculates a chi-square p value by simply calculating: `1 - pchisq(resReduced$deviance - resFull$deviance, attr(resReduced, "df.residual") - attr(resFull, "df.residual"))`

### Usage

    nbinomGLMTest(resFull, resReduced)

### Arguments

`resFull, resReduced` | GLM fit data frames, as returned by `fitNbinomGLMs`, first the full, then the reduced model.

### Value

a vector of p values

### Author(s)

Simon Anders, anders@embl.de

### See Also

`fitNbinomGLMs`

### Examples

    cds <- makeExampleCountDataSet()[ 1:100, ]
    cds <- estimateSizeFactors( cds )
    cds <- estimateDispersions( cds, method="pooled" )
    fit1 <- fitNbinomGLMs( cds, count ~ condition )
    fit0 <- fitNbinomGLMs( cds, count ~ 1 )
    nbinomGLMTest( fit1, fit0 )

[Package DESeq version 1.39.0 Index]