Calls outliers.
# S3 method for CBS
callOutliers(fit, adjust=1, method=c("ucsf-mad"), ...)Returns a CBS object where logical columns
'negOutlierCall' and 'posOutlierCall' have been appended
to the segmentation table.
A positive scale factor adjusting the sensitivity of the caller, where a value less (greater) than 1.0 makes the caller less (more) sensitive.
A character string specifying the calling algorithm to use.
Additional/optional arguments used to override the default parameters used by the caller.
If method == "ucsf-mad", then loci are called using [1]
"Finally, to identify single technical or biological outliers such
as high level amplifications, the presence of the outliers within
a segment was allowed by assigning the original observed log2ratio
to the clones for which the observed values were more than four
tumor-specific MAD away from the smoothed values." [1; Suppl. Mat.]
Henrik Bengtsson
[1] Fridlyand et al. Breast tumor copy number aberration
phenotypes and genomic instability, BMC Cancer, 2006.
*callGainsAndLosses().
*callAmplifications().
For more information see CBS.