callLOH.PairedPSCBS: Calls segments that are in LOH

In HenrikBengtsson/PSCBS: Analysis of Parent-Specific DNA Copy Numbers

Calls segments that are in LOH

Description

Calls segments that are in LOH, i.e. that have "zero" minor copy number.

Usage

## S3 method for class 'PairedPSCBS'
callLOH(fit, flavor=c("SmallC1", "LargeDH"), ..., minSize=1, xorCalls=TRUE, force=FALSE)

Arguments

flavor	A character string specifying which type of call to use.
...	Additional arguments passed to the caller.
minSize	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.
xorCalls	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).
force	If FALSE, and allelic-balance calls already exits, then nothing is done, otherwise the calls are done.

Value

Returns a PairedPSCBS object with LOH calls.

AB and LOH consistency

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.

Author(s)

Henrik Bengtsson

See Also

Internally, one of the following methods are used: *callLowC1ByC1(), *callExtremeAllelicImbalanceByDH().

HenrikBengtsson/PSCBS documentation built on Feb. 20, 2024, 9:01 p.m.