intansv (version 1.10.0)

readBreakDancer: Read in the structural variations predicted by breakDancer

Description

Reading in the structural variations predicted by breakDancer, filtering low quality predictions and merging overlapping predictions.

Usage

readBreakDancer(file="", scoreCutoff=60, readsSupport=3,  regSizeLowerCutoff=100, regSizeUpperCutoff=1000000, method="BreakDancer", ...)

Arguments

file

the output file of breakDancer.

scoreCutoff

the minimum score for a structural variation to be read in.

readsSupport

the minimum read pair support for a structural variation to be read in.

regSizeLowerCutoff

the minimum size for a structural variation to be read in.

regSizeUpperCutoff

the maximum size for a structural variation to be read in.

method

a tag to assign to the result of this function.

...

parameters passed to read.table.

Value

A list with the following components:

del

the deletions predicted by breakDancer.

inv

the inversions predicted by breakDancer.

Details

The predicted SVs could be further filtered by score, number of read pairs supporting the occurence of a specific SV, and the predicted size of SVs to get more reliable SVs. See our paper for more details.

Examples

    breakdancer <- readBreakDancer(system.file("extdata/ZS97.breakdancer.sv",
                                   package="intansv"))
    str(breakdancer)