readDelly {intansv} | R Documentation

## Read in the structural variations predicted by DELLY

### Description

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

### Usage

        readDelly(dataDir=".", regSizeLowerCutoff=100,
                  regSizeUpperCutoff=10000000, readsSupport=3,
                  method="DELLY", pass=TRUE, minMappingQuality=20)

### Arguments

`dataDir` | a directory containing the prediction results of DELLY.
`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.
`pass` | set pass=TRUE to remove LowQual SVs reported by DELLY.
`minMappingQuality` | the minimum mapping quality for a SV to be read.

### Details

The predicted SVs could be further filtered by the 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. The directory that specified by the parameter "dataDir" should only contain the predictions of DELLY. See the example dataset for more details.

### Value

A list with the following components:

`del` | the deletions predicted by DELLY.
`dup` | the duplications predicted by DELLY.
`inv` | the inversions predicted by DELLY.

### Author(s)

Wen Yao

### Examples

        delly <- readDelly(system.file("extdata/delly",package="intansv"))
        str(delly)

[Package intansv version 1.24.0 Index]