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

1
2
3
    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.

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.

Value

A list with the following components:

del

the deletions predicted by breakDancer.

inv

the inversions predicted by breakDancer.

Author(s)

Wen Yao

Examples

1
2
3
    breakdancer <- readBreakDancer(system.file("extdata/ZS97.breakdancer.sv",
                                   package="intansv"))
    str(breakdancer)