quickEnhancers: Identify and quantify enhancers.

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

Identify and quantify enhancers.

Description

A convenient wrapper to the function CAGEfightR::quickEnhancers().

Usage

quickEnhancers(object)

## S4 method for signature 'CAGEexp'
quickEnhancers(object)

Arguments

object

A CAGEexp object

Details

The CAGEr object will be converted to a format similar to the output of CAGEfightR::quantifyCTSSs(), and then passed to the quickEnhancers function.

Value

A RangedSummarizedExperiment object. See the example below on how to attach it to the experiment list of a CAGEexp object.

Note

At the moment the conversion is expensive as it goes from DataFrame of Rle to data.frame to matrix.

See Also

Other CAGEr object modifiers: CTSStoGenes(), CustomConsensusClusters(), aggregateTagClusters(), annotateCTSS(), cumulativeCTSSdistribution(), distclu(), getCTSS(), normalizeTagCount(), paraclu(), quantilePositions(), resetCAGEexp(), summariseChrExpr()

Examples

# Can not run as long as the test data has nothing on the minus strand!
## Not run: 
quickEnhancers(exampleCAGEexp)

## End(Not run)

charles-plessy/CAGEr documentation built on Aug. 2, 2024, 4:35 p.m.