consensusClustersDESeq2: Export _consensus cluster_ expression data for DESeq2...

In charles-plessy/CAGEr: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining

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 '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(), tagClustersGR()

Examples

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

charles-plessy/CAGEr documentation built on Nov. 4, 2023, 11:57 a.m.