GeneExpDESeq2 {CAGEr} | R Documentation

## Export gene expression data for DESeq2 analysis

### Description

Creates a `DESeqDataSet` using the gene expression data in the experiment slot `geneExpMatrix` and the sample metadata of the `CAGEexp` object. The formula must be built using factors already present in the sample metadata.

### Usage

    GeneExpDESeq2(object, design)

    ## S4 method for signature 'CAGEset'
    GeneExpDESeq2(object, design)

    ## S4 method for signature 'CAGEexp'
    GeneExpDESeq2(object, design)

### Arguments

`object` | A `CAGEexp` object.
`design` | A formula for the DESeq2 analysis.

### Author(s)

Charles Plessy

### See Also

`DESeqDataSet` in the `DESeq2` package.

Other CAGEr gene expression analysis functions: `CTSStoGenes`, `ranges2genes`

Other CAGEr accessor methods: `CTSSclusteringMethod`, `CTSScoordinates`, `CTSScumulativesTagClusters`, `CTSSnormalizedTpm`, `CTSStagCountTable`, `CTSStagCount`, `GeneExpSE`, `consensusClustersGR`, `genomeName`, `inputFilesType`, `inputFiles`, `librarySizes`, `sampleLabels`, `seqNameTotalsSE`, `tagClusters`

### Examples

    exampleCAGEexp$group <- factor(c("a", "a", "b", "b", "a"))
    GeneExpDESeq2(exampleCAGEexp, ~group)

[Package CAGEr version 1.28.0 Index]