readDelly: Read in the structural variations predicted by DELLY

In venyao/intansv: Integrative analysis of structural variations

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

Arguments

file	the file 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.
...	parameters passed to read.table.

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.

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/ZS97.DELLY.vcf",package="intansv"))
    str(delly)

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