combineClusters: Combine two CAGE experiments.

Description Usage Arguments Value Examples

Description

This function can safely combine two CAGE experiments, for example TCs and enhancers, for later analysis, by making sure no ranges in the final object are overlapping.

Usage

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combineClusters(object1, object2, ...)

## S4 method for signature 
## 'RangedSummarizedExperiment,RangedSummarizedExperiment'
combineClusters(object1, object2, removeIfOverlapping = "none")

Arguments

object1

RangedSummarizedExperiment: First experiment to be combined.

object2

RangedSummarizedExperiment: First experiment to be combined.

...

arguments passed to methods.

removeIfOverlapping

character: Whether to keep overlapping ranges ('none') or discard from either the first ('object1') or second ('object2') experiment.

Value

RangedSummarizedExperiment with merged and sorted ranges (colData and metadata are carried over unchanged).

Examples

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data(exampleUnidirectional)
data(exampleBidirectional)

# Clusters must have identical colData to be combined:
exampleUnidirectional$totalTags <- NULL

# Combine, keeping potential overlaps
combineClusters(object1=exampleUnidirectional, object2=exampleBidirectional)

# If features overlap, keep only from object1
combineClusters(object1=exampleUnidirectional, object2=exampleBidirectional,
   removeIfOverlapping='object2')

# If features overlap, keep only from object2
combineClusters(object1=exampleUnidirectional, object2=exampleBidirectional,
   removeIfOverlapping='object1')

MalteThodberg/CAGEfightR documentation built on Sept. 11, 2021, 4:42 a.m.