tagClusters {CAGEr}R Documentation

Extract tag clusters (TCs) for individual CAGE experiments

Description

Extracts tag clusters (TCs) produced by clusterCTSS function for a specified CAGE experiment from a CAGEr object.

Usage

tagClusters(object, samples = NULL, returnInterquantileWidth = FALSE,
  qLow = NULL, qUp = NULL)

## S4 method for signature 'CAGEr'
tagClusters(object, samples = NULL,
  returnInterquantileWidth = FALSE, qLow = NULL, qUp = NULL)

tagClustersGR(object, sample = NULL, returnInterquantileWidth = FALSE,
  qLow = NULL, qUp = NULL)

## S4 method for signature 'CAGEset'
tagClustersGR(object, sample = NULL,
  returnInterquantileWidth = FALSE, qLow = NULL, qUp = NULL)

## S4 method for signature 'CAGEexp'
tagClustersGR(object, sample = NULL,
  returnInterquantileWidth = FALSE, qLow = NULL, qUp = NULL)

tagClustersGR(object, samples = NULL) <- value

## S4 replacement method for signature 'CAGEset,ANY,ANY'
tagClustersGR(object,
  samples = NULL) <- value

## S4 replacement method for signature 'CAGEexp,ANY,TagClusters'
tagClustersGR(object,
  samples = NULL) <- value

## S4 replacement method for signature 'CAGEexp,missing,GRangesList'
tagClustersGR(object,
  samples = NULL) <- value

Arguments

object

A CAGEr object.

samples

Label of the CAGE dataset (experiment, sample) for which to extract tag clusters. If samples = NULL, a list of all the clusters for each sample is returned.

returnInterquantileWidth

Should the interquantile width for each tag cluster be returned.

qLow, qUp

Position of which quantile should be used as a left (lower) or right (upper) boundary (for qLow and qUp respectively) when calculating interquantile width. Default value NULL results in using the start coordinate of the cluster. Used only when returnInterquantileWidth = TRUE, otherwise ignored.

sample

Label of one CAGE dataset (experiment, sample) for which to extract tag clusters. (For tagClustersGR, only one sample can be extracted.)

value

A TagClusters object.

Value

Returns a data.frame with genomic coordinates, position of dominant TSS, total CAGE signal and additional information for all TCs from specified CAGE dataset (sample). If returnInterquantileWidth = TRUE, interquantile width for each TC is also calculated using specified quantile positions and returned in the data frame.

Author(s)

Vanja Haberle

See Also

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

Other CAGEr clusters functions: CTSSclusteringMethod, CTSScumulativesTagClusters, CustomConsensusClusters, aggregateTagClusters, clusterCTSS, consensusClustersDESeq2, consensusClustersGR, cumulativeCTSSdistribution, plotInterquantileWidth, quantilePositions

Examples

head(tagClusters( exampleCAGEset, "sample2"
                , returnInterquantileWidth = TRUE, qLow = 0.1, qUp = 0.9))
tagClustersGR(exampleCAGEexp, "Zf.high", TRUE, 0.1, 0.9)
[Package CAGEr version 1.29.2 Index]