exportRegions: Function to print WC regions after breakpointR analysis

In daewoooo/breakpointR: Find breakpoints in Strand-seq data

Function to print WC regions after breakpointR analysis

Description

Function to print WC regions after breakpointR analysis

Usage

exportRegions(
  datapath,
  file = NULL,
  collapseInversions = FALSE,
  collapseRegionSize = 5e+06,
  minRegionSize = 5e+06,
  state = "wc"
)

Arguments

datapath	A path to that
file	A filename to print exported regions to.
collapseInversions	Set to TRUE if you want to collapse putative inverted regions.
collapseRegionSize	Upper range of what sized regions should be collapsed.
minRegionSize	Minimal size of the region to be reported.
state	A genotype of the regions to be exported ('ww', 'cc' or 'wc').

Value

A data.frame object containing all regions with user defined 'state'.

Author(s)

David Porubsky

Examples

## Get an example file
exampleFolder <- system.file("extdata", "example_results", package="breakpointRdata")
## To export regions genotyped as 'wc'
wc.regions <- exportRegions(datapath=exampleFolder, collapseInversions=FALSE, minRegionSize=5000000, state='wc') 

daewoooo/breakpointR documentation built on April 20, 2023, 4:13 p.m.