tagClusters: Extract tag clusters (TCs) for individual CAGE experiments

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

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)

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