CTSStoGenes {CAGEr}R Documentation

Make a gene expression table.

Description

Add a gene expression table in the GeneExpSE experiment slot of an annotated CAGEexp object.

Usage

CTSStoGenes(object)

## S4 method for signature 'CAGEexp'
CTSStoGenes(object)

Arguments

object

A CAGEexp object that was annotated with the annotateCTSS() function.

Value

The input object with the following modifications:

Author(s)

Charles Plessy

See Also

annotateCTSS().

Other CAGEr object modifiers: CustomConsensusClusters(), aggregateTagClusters(), annotateCTSS(), clusterCTSS(), cumulativeCTSSdistribution(), getCTSS(), normalizeTagCount(), quantilePositions(), summariseChrExpr()

Other CAGEr gene expression analysis functions: GeneExpDESeq2(), ranges2genes()

Examples

CTSStoGenes(exampleCAGEexp)
all( librarySizes(exampleCAGEexp) -
     colSums(SummarizedExperiment::assay(GeneExpSE(exampleCAGEexp))) ==
     exampleCAGEexp$unannotated)


[Package CAGEr version 2.0.1 Index]