breakpointr2UCSC: Export UCSC browser formated files

In breakpointR: Find breakpoints in Strand-seq data

Description

Write a bedfile or bedgraph from a breakpointR object for upload on to the UCSC Genome browser.

Usage

breakpointr2UCSC(
  index,
  outputDirectory,
  fragments = NULL,
  deltaWs = NULL,
  breakTrack = NULL,
  confidenceIntervals = NULL,
  breaksGraph = NULL
)

Arguments

index	A character used to name the bedfile(s).
outputDirectory	Location to write bedfile(s).
fragments	A GRanges-class object with strand and mapq metadata, such as that generated by readBamFileAsGRanges
deltaWs	A GRanges-class object with metadata column "deltaW" generated by deltaWCalculator.
breakTrack	A GRanges-class object with metadata "genoT" (e.g. newBreaks) will write a bedtrack with refined breakpoints.
confidenceIntervals	A GRanges-class object with metadata "genoT" the same length as breakTrack (e.g. confint) will write a bedtrack with breakpoints confidence intervals.
breaksGraph	A GRanges-class object.

Value

NULL

Author(s)

Ashley Sanders, David Porubsky, Aaron Taudt

Examples

## Get an example file
exampleFolder <- system.file("extdata", "example_results", package="breakpointRdata")
exampleFile <- list.files(exampleFolder, full.names=TRUE)[1]
## Load the file 
brkpts <- get(load(exampleFile))
## Write results to BED files
breakpointr2UCSC(index='testfile', outputDirectory=tempdir(), breakTrack=brkpts$breaks)

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