readSoftSearch: Read in the structural variations predicted by SoftSearch

In venyao/intansv: Integrative analysis of structural variations

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

    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)

venyao/intansv documentation built on Jan. 3, 2024, 6:15 p.m.