readSoftSearch: 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
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.
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.
Examples
Run this code
softSearch <- readSoftSearch(system.file("extdata/ZS97.softsearch",package="intansv"))
str(softSearch)
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