readSoftSearch: Read in the structural variations predicted by SoftSearch

Description Usage Arguments Details Value Author(s) Examples

Description

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

Usage

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    readSoftSearch(file="", regSizeLowerCutoff=100, readsSupport=3, 
                   method="softSearch", regSizeUpperCutoff=1000000, 
                   softClipsSupport=3, ...) 

Arguments

file

the file containing the prediction results of SoftSearch.

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.

softClipsSupport

the minimum soft clip support for a structural variation to be read.

...

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 SoftSearch.

dup

the duplications predicted by SoftSearch.

inv

the inversions predicted by SoftSearch.

Author(s)

Wen Yao

Examples

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    softSearch <- readSoftSearch(system.file("extdata/ZS97.softsearch",package="intansv"))
    str(softSearch)


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