readSoftSearch: Read in the structural variations predicted by SoftSearch

In intansv: Integrative analysis of structural variations

Description

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

Usage

    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

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

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