readDelly: Read in the structural variations predicted by DELLY

View source: R/readDelly.R

readDellyR 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(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.