Calls (focal) amplifications.
# S3 method for CBS
callAmplifications(fit, adjust=1, maxLength=2e+07, method=c("ucsf-exp"), ...,
verbose=FALSE)Returns a CBS object where logical column
'amplificationCall' has 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 double scalar specifying the maximum length of a segment
in order for it to be considered a focal amplification.
A character string specifying the calling algorithm to use.
Additional/optional arguments used to override the default parameters used by the caller.
Verbose.
If method == "ucsf-exp", then segments are called using [1], i.e.
a segment is called an amplification if ...
Henrik Bengtsson
[1] Fridlyand et al. Breast tumor copy number aberration
phenotypes and genomic instability, BMC Cancer, 2006.
*callGainsAndLosses().
*callOutliers().
For more information see CBS.