consensusClusters: Extracting consensus clusters from CAGEset object

In ge11232002/CAGEr: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining

Description

Extracts the information on consensus clusters from a CAGEset object.

Usage

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

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

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

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

ge11232002/CAGEr documentation built on May 17, 2019, 12:13 a.m.