librarySizes: Extracting library sizes from CAGEr objects

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

Description

Extracts the library sizes (total number of CAGE tags) for all CAGE datasets from CAGEset and CAGEexp objects.

Usage

librarySizes(object)

## S4 method for signature 'CAGEset'
librarySizes(object)

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

Arguments

object

A CAGEset or CAGEexp object.

Details

Library sizes are calculated when loading data with the getCTSS function and stored in the librarySizes slot of CAGEset objects, or in the librarySizes column of the colData ov CAGEexp objects.

Value

Returns an integer vector of total number of CAGE tags (library size) for all CAGE datasets in the CAGEr object.

Author(s)

Vanja Haberle

See Also

getCTSS

Other CAGEr accessor methods: CTSSclusteringMethod, CTSScoordinates, CTSScumulativesTagClusters, CTSSnormalizedTpm, CTSStagCountTable, CTSStagCount, GeneExpDESeq2, GeneExpSE, consensusClustersGR, genomeName, inputFilesType, inputFiles, sampleLabels, seqNameTotalsSE, tagClusters

Examples

librarySizes(exampleCAGEset)

CAGEr documentation built on Jan. 17, 2021, 2 a.m.