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

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

Extract tag clusters (TCs) for individual CAGE experiments

Description

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

Usage

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, sample = NULL) <- value

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

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

Arguments

object	A CAGEexp object.
sample	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	Return the interquantile width for each tag cluster.
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.
value	A TagClusters object.

Value

Returns a GRangesList or a GRanges object 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 provided quantile positions. The S4Vectors::metadata slot of the object contains a copy of the CAGEexp object's column data, as well as information on the clustering method in a clusteringMethod element.

Author(s)

Vanja Haberle

Charles Plessy

See Also

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

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

Examples

tagClustersGR( exampleCAGEexp, "Zf.high", TRUE, 0.1, 0.9 )
tagClustersGR( exampleCAGEexp, 1
             , returnInterquantileWidth = TRUE, qLow = 0.1, qUp = 0.9 )
tagClustersGR( exampleCAGEexp )@metadata$colData

charles-plessy/CAGEr documentation built on Nov. 4, 2023, 11:57 a.m.