readBreakDancer {intansv} | R Documentation |
Reading in the structural variations predicted by breakDancer, filtering low quality predictions and merging overlapping predictions.
readBreakDancer(file="", scoreCutoff=60, readsSupport=3, regSizeLowerCutoff=100, regSizeUpperCutoff=10000000, method="BreakDancer", ...)
file |
the output file of breakDancer. |
scoreCutoff |
the minimum score for a structural variation to be read in. |
readsSupport |
the minimum read pair support for a structural variation to be read in. |
regSizeLowerCutoff |
the minimum size for a structural variation to be read in. |
regSizeUpperCutoff |
the maximum size for a structural variation to be read in. |
method |
a tag to assign to the result of this function. |
... |
parameters passed to read.table. |
The predicted SVs could be further filtered by score, number of read pairs 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 breakDancer. |
inv |
the inversions predicted by breakDancer. |
Wen Yao
breakdancer <- readBreakDancer(system.file("extdata/ZS97.breakdancer.sv", package="intansv")) str(breakdancer)