GeneExpDESeq2: Export gene expression data for DESeq2 analysis

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 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 '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: CTSScoordinatesGR(), CTSScumulativesTagClusters(), CTSSnormalizedTpmDF(), CTSStagCountDF(), GeneExpSE(), consensusClustersGR(), expressionClasses(), filteredCTSSidx(), genomeName(), inputFiles(), inputFilesType(), librarySizes(), sampleLabels(), seqNameTotalsSE(), tagClustersGR()

Examples

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

charles-plessy/CAGEr documentation built on Oct. 27, 2024, 10:11 p.m.