CAGEr (version 1.14.0)

tagClusters: Extracting tag clusters (TCs) for individual CAGE experiment from CAGEset object

Description

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

Usage

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

Arguments

object

A CAGEset object

sample

Label of the CAGE dataset (experiment, sample) for which to extract tag clusters.

returnInterquantileWidth

Should the interquantile width for each tag cluster be returned.

qLow

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

qUp

Position of which quantile should be used as a right (upper) boundary when calculating interquantile width. Default value NULL results in using the end coordinate of the cluster. Used only when returnInterquantileWidth = TRUE, otherwise ignored.

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.

See Also

clusterCTSS

Examples

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

TC <- tagClusters(object = exampleCAGEset, sample = "sample2", returnInterquantileWidth = TRUE, qLow = 0.1, qUp = 0.9)
head(TC)