Read in the structural variations predicted by SoftSearch

Description

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

Usage

1
2
3
    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

1
2
    softSearch <- readSoftSearch(system.file("extdata/ZS97.softsearch",package="intansv"))
    str(softSearch)