read.breakdancer: Illustrative function to read the output of Breakdancer.

In jjellis/GenomicVis: Genomic Visualisation Routines

Description

This function reads a Breakdancer output file and returns a data.frame suitable as input to cnv.plot. This only serves as an example, Breakdancer output is not required to run cnv.plot, the structural variant data may come from any source.

Usage

read.breakdancer(f, chrom = NA, normal.regex = "NORMAL",
  tumour.regex = "TUMOUR")

Arguments

f	The Breakdancer output file name
chrom	The chromosome to process
normal.regex	A regular expression used on the input file names to identify the normal sample.
tumour.regex	A regular expression used on the input file names to identify the tumour sample.

Value

A data.frame suitable as input to cnv.plot

Author(s)

Jonathan Ellis <[e-mail]>

Examples

## Not run: 
read.breakdancer()

## End(Not run)

jjellis/GenomicVis documentation built on May 19, 2019, 11:39 a.m.