Read in the structural variations predicted by CNVnator

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Description

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

Usage

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    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

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