readSoftSearch {intansv} | R Documentation |
Reading the structural variations predicted by SoftSearch, filtering low quality predictions and merging overlapping predictions.
readSoftSearch(file="", regSizeLowerCutoff=100, readsSupport=3, method="softSearch", regSizeUpperCutoff=1000000, softClipsSupport=3, ...)
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 |
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.
A list with the following components:
del |
the deletions predicted by SoftSearch. |
dup |
the duplications predicted by SoftSearch. |
inv |
the inversions predicted by SoftSearch. |
Wen Yao
softSearch <- readSoftSearch(system.file("extdata/ZS97.softsearch",package="intansv")) str(softSearch)