readLumpy: Read in the structural variations predicted by Lumpy

Description

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

Usage

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    readLumpy(file="", regSizeLowerCutoff=100, readsSupport=3, 
              method="Lumpy", regSizeUpperCutoff=1000000, 
              breakpointThres=200, scoreCut=0.1, ...)

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.

breakpointThres

a threshold to remove SVs with breakpoint with too large interval.

scoreCut

predictions with score larger than this threshold will be discarded.

...

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

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    lumpy <- readLumpy(system.file("extdata/ZS97.lumpy.pesr.bedpe",package="intansv"))
    str(lumpy)

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.