Extracting consensus clusters from CAGEset object

Description

Extracts the information on consensus clusters from a CAGEset object.

Usage

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

Arguments

object

A CAGEset object

sample

Optional. Label of the CAGE dataset (experiment, sample) for which to extract sample-specific information on consensus clusters.

returnInterquantileWidth

Should the interquantile width of consensus clusters in specified sample be returned. Used only when sample argument is specified, otherwise ignored.

qLow

Position of which quantile should be used as a left (lower) boundary when calculating interquantile width. Used only when sample argument is specified and returnInterquantileWidth = TRUE, otherwise ignored.

qUp

Position of which quantile should be used as a right (upper) boundary when calculating interquantile width. Used only when sample argument is specified and returnInterquantileWidth = TRUE, otherwise ignored.

Value

Returns a data.frame with information on consensus clusters, including genomic coordinates. When sample argument is NOT specified, total CAGE signal across all CAGE datasets (samples) is returned in the tpm column. When sample argument is specified, the tpm column contains CAGE signal of consensus clusters in that specific sample. When returnInterquantileWidth = TRUE, additional sample-specific information is returned, including position of the dominant TSS, and interquantile width of the consensus clusters in the specified sample.

Author(s)

Vanja Haberle

See Also

tagClusters

Examples

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load(system.file("data", "exampleCAGEset.RData", package="CAGEr"))

clusters.general <- consensusClusters(exampleCAGEset)
head(clusters.general)

clusters.sample <- consensusClusters(exampleCAGEset, sample = "sample2")
head(clusters.sample)

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