readPindel: Read in the structural variations predicted by Pindel

In venyao/intansv: Integrative analysis of structural variations

Read in the structural variations predicted by Pindel

Description

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

Usage

    readPindel(dataDir=".", regSizeLowerCutoff=100, 
               regSizeUpperCutoff=1000000, readsSupport=3,
               method="Pindel")

Arguments

dataDir	the directory containing the prediction results of Pindel.
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.

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. The directory that specified by the parameter "dataDir" should only contain the predictions of Pindel. The deletions output files should be named using the suffix "_D", the duplications output files should be named using the suffix "_TD", and the inversions output files should be named using the suffix "_INV". See the example dataset for more details.

Value

A list with the following components:

del	the deletions predicted by Pindel.
dup	the duplications predicted by Pindel.
inv	the inversions predicted by Pindel.

Author(s)

Wen Yao

Examples

    pindel <- readPindel(system.file("extdata/pindel",package="intansv"))
    str(pindel)

venyao/intansv documentation built on Jan. 3, 2024, 6:15 p.m.