sampleLabels: Get and set sample labels

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

Description

sampleLabels gets or sets the labels and colors of CAGE datasets (samples) from CAGEr objects.

sampleList is an accessory function for convenience iteration in functions such as lapply or mapply. There is no set method for sampleList.

Usage

sampleLabels(object)

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

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

## S4 method for signature 'CTSS'
sampleLabels(object)

sampleList(object)

## S4 method for signature 'CAGEr'
sampleList(object)

sampleLabels(object) <- value

## S4 replacement method for signature 'CAGEset'
sampleLabels(object) <- value

## S4 replacement method for signature 'CAGEexp'
sampleLabels(object) <- value

## S4 replacement method for signature 'CTSS'
sampleLabels(object) <- value

Arguments

object	A CAGEr object.
value	A character vector with a unique and valid name for each sample. The names attributes indicate the colors.

Details

In CAGEexp objects, renaming samples is possible only before data is loaded.

Value

sampleLabels returns a named character vector representing labels of all CAGE datasets present in the CAGEr object. The vector values are the labels and the vector names are the colors.

sampleList returns a named list where elements and their names are the sample names, for instance: list(sampleA = "sampleA", sampleB = "sampleB"). Thus, after iterating on it with lapply, the element names will be sample names.

Note

If no colors are supplied, then default colors will be assigned usign the rainbow function. Assigned colors are not guaranteed to be stable.

Author(s)

Vanja Haberle

Charles Plessy

See Also

setColors

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

Other CAGEr setter methods: genomeName, inputFilesType, inputFiles, setColors

Examples

sampleLabels(exampleCAGEset)

sampleList(exampleCAGEset)

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