Calls segments that are in LOH, i.e. that have "zero" minor copy number.
# S3 method for PairedPSCBS
callLOH(fit, flavor=c("SmallC1", "LargeDH"), ..., minSize=1, xorCalls=TRUE, force=FALSE)Returns a PairedPSCBS object with LOH calls.
A character string specifying which type of
call to use.
Additional arguments passed to the caller.
An optional integer specifying the minimum number
of data points in order to call a segments. If fewer data points,
then the call is set to NA regardless.
If TRUE, a region already called AB, will
for consistency never be called LOH, resulting in either an LOH
call set to FALSE or NA (as explained below).
If FALSE, and allelic-balance calls already exits,
then nothing is done, otherwise the calls are done.
Biologically, a segment can not be both in allelic balance (AB) and
in loss-of-heterozygosity (LOH) at the same time.
To avoid reporting such inconsistencies, the LOH caller will,
if argument xorCalls=TRUE, never report a segment to be in
LOH if it is already called to be in AB.
However, regardless of of the AB call, a segment is still always
tested for LOH, to check weather the LOH caller is consistent with the
AB caller or not. Thus, in order to distinguish the case where
the AB caller and LOH caller agree from when they disagree,
we report either (AB,LOH)=(TRUE,FALSE) or (TRUE,NA). The former is
reported when they are consistent, and the latter when they are not,
or when the LOH caller could not call it.
Henrik Bengtsson
Internally, one of the following methods are used:
*callLowC1ByC1(),
*callExtremeAllelicImbalanceByDH().