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. CAGEset objects are not supported.

Usage

CTSStoGenes(object)

## S4 method for signature 'CAGEset'
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 1.24.0 Index]