consensusClustersDESeq2 {CAGEr} | R Documentation

## Export consensus cluster expression data for DESeq2 analysis

### Description

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

### Usage

    consensusClustersDESeq2(object, design)

    ## S4 method for signature 'CAGEset'
    consensusClustersDESeq2(object, design)

    ## S4 method for signature 'CAGEexp'
    consensusClustersDESeq2(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 clusters functions: `CTSSclusteringMethod`, `CTSScumulativesTagClusters`, `CustomConsensusClusters`, `aggregateTagClusters`, `clusterCTSS`, `consensusClustersGR`, `cumulativeCTSSdistribution`, `plotInterquantileWidth`, `quantilePositions`, `tagClusters`

### Examples

    exampleCAGEexp$group <- c("a", "a", "b", "b", "a")
    consensusClustersDESeq2(exampleCAGEexp, ~group)

[Package CAGEr version 1.28.0 Index]