readLumpy {intansv} | R Documentation

## Read in the structural variations predicted by Lumpy

### Description

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

### Usage

        readLumpy(file="", regSizeLowerCutoff=100, regSizeUpperCutoff=1000000,
    	readsSupport=3, method="Lumpy",  ...)

### Arguments

`file` | the file containing the prediction results of Lumpy.
`regSizeLowerCutoff` | the minimum size for a structural variation to be read.
`regSizeUpperCutoff` | the maximum size for a structural variation to be read.
`readsSupport` | the minimum read pair support for a structural variation to be read.
`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 the number of reads 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 Lumpy.
`dup` | the duplications predicted by Lumpy.
`inv` | the inversions predicted by Lumpy.

### Author(s)

Wen Yao

### Examples

        lumpy <- readLumpy(system.file("extdata/ZS97.lumpy.pesr.bedpe",package="intansv"))
        str(lumpy)

[Package intansv version 1.22.0 Index]