Usage
readLumpy(file="", regSizeLowerCutoff=100, readsSupport=3, method="Lumpy", regSizeUpperCutoff=1000000, breakpointThres=200, scoreCut=0.1, ...)
Arguments
file
the file containing the prediction results of Lumpy.
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.
breakpointThres
a threshold to remove SVs with breakpoint with
too large interval.
scoreCut
predictions with score larger than this threshold will
be discarded.
...
parameters passed to read.table.