readLumpy: Read in the structural variations predicted by Lumpy

In intansv: Integrative analysis of structural variations

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.vcf",package="intansv"))
    str(lumpy)

intansv documentation built on Nov. 8, 2020, 5:15 p.m.