removeReadPileupSpikes: Remove large spikes in short reads coverage

In breakpointR: Find breakpoints in Strand-seq data

Description

This function takes a GRanges-class object of aligned short reads and removes pockets of reads that are stacked on top of each other based on the maximum number of reads allowed to pileup in 'max.pileup' parameter.

Usage

removeReadPileupSpikes(gr = NULL, max.pileup = 30)

Arguments

gr	A GRanges-class object.
max.pileup	A maximum number of reads overlapping each other to be kept.

Value

A GRanges-class object.

Author(s)

David Porubsky

Examples

## Get some files that you want to load
exampleFolder <- system.file("extdata", "example_results", package="breakpointRdata")
infile <- list.files(exampleFolder, full.names=TRUE)[1]
## Read in the reads
breakP.obj <- get(load(infile))
frags <- breakP.obj$fragments 
## Remove read spikes
frags <- removeReadPileupSpikes(gr=frags)

breakpointR documentation built on Nov. 8, 2020, 8:04 p.m.