readCnvnator: Read in the structural variations predicted by CNVnator

In intansv: Integrative analysis of structural variations

Description

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

Usage

    readCnvnator(dataDir=".", regSizeLowerCutoff=100, regSizeUpperCutoff=1000000,
                 method="CNVnator")

Arguments

dataDir	the directory that contain the output files of CNVnator.
regSizeLowerCutoff	the minimum size for a structural variation to be read.
regSizeUpperCutoff	the maximum size 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 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 CNVnator. See the example dataset for more details.

Value

A list with the following components:

del	the deletions predicted by CNVnator.
dup	the duplications predicted by CNVnator.

Author(s)

Wen Yao

Examples

    cnvnator <- readCnvnator(system.file("extdata/cnvnator",package="intansv"))
    str(cnvnator)

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