tagClusters: Extracting tag clusters (TCs) for individual CAGE experiment...

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 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.

Author(s)

Vanja Haberle

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)

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