seqNameTotalsSE: Retreives the SummarizedExperiment containing chromosome...

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

Retreives the SummarizedExperiment containing chromosome expression totals.

Description

Get or set a SummarizedExperiment summarising whole-chromosome expression levels in the experiment slot seqNameTotals and the sample metadata of the CAGEexp object.

Usage

seqNameTotalsSE(object)

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

seqNameTotalsSE(object) <- value

Arguments

object	A CAGEexp object.
value	A SummarizedExperiment object where rows represent reference sequences such as chromosomes.

Author(s)

Charles Plessy

See Also

summariseChrExpr

Other CAGEr accessor methods: CTSScoordinatesGR(), CTSScumulativesTagClusters(), CTSSnormalizedTpmDF(), CTSStagCountDF(), GeneExpDESeq2(), GeneExpSE(), consensusClustersGR(), expressionClasses(), filteredCTSSidx(), genomeName(), inputFiles(), inputFilesType(), librarySizes(), sampleLabels(), tagClustersGR()

Examples

seqNameTotalsSE(exampleCAGEexp)

charles-plessy/CAGEr documentation built on Aug. 2, 2024, 4:35 p.m.