extractExpressionClass: Extract elements of the specified expression class

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

Description

Extracts CTSSs or consensus clusters belonging to a specified expression class.

Usage

extractExpressionClass(object, what, which = "all")

## S4 method for signature 'CAGEexp'
extractExpressionClass(object, what, which = "all")

## S4 method for signature 'CAGEset'
extractExpressionClass(object, what, which = "all")

Arguments

object	A CAGEset object.
what	Which level of expression clustering should be used. Can be either "CTSS" to extract expression class of individual CTSSs or "consensusClusters" to extract expression class of consensus clusters.
which	Which expression class should be extracted. It has to be one of the valid expression class labels (as returned by expressionClasses function), or "all" to extract members of all expression classes.

Value

Returns a data.frame of CTSSs (when what = "CTSS") or consensus clusters (when what = "consensusClusters") belonging to a specified expression class, with genomic coordinates and additional information. Last column contains the label of the corresponding expression class.

Author(s)

Vanja Haberle

See Also

getExpressionProfiles, plotExpressionProfiles, expressionClasses.

Examples

CTSSexprClasses <- extractExpressionClass(exampleCAGEset, what = "CTSS", which = "all")
head(CTSSexprClasses)

CAGEr documentation built on Jan. 17, 2021, 2 a.m.