combineClusters: Combine two CAGE experiments.

In MalteThodberg/CAGEfightR: Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor

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

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

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.