readBreakDancer {intansv} | R Documentation

## 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=10000000,
                        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

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

[Package intansv version 1.24.0 Index]