callAmplifications.CBS: Calls (focal) amplifications
Description
Calls (focal) amplifications.Usage
## S3 method for class 'CBS':
callAmplifications(fit, adjust=1, maxLength=2e+07, method=c("ucsf-exp"), ...,
verbose=FALSE)Arguments
adjust
A positive scale factor adjusting the sensitivity of the
caller, where a value less (greater) than 1.0 makes the caller
less (more) sensitive.
maxLength
A double scalar specifying the maximum length of a segment
in order for it to be considered a focal amplification. method
A character string specifying the calling algorithm to use. ...
Additional/optional arguments used to override the default
parameters used by the caller.
Value
- Returns a
CBS object where logical column
'amplificationCall' has been appended to the segmentation table.
The UCSF caller
If method == "ucsf-exp", then segments are called using [1], i.e.
a segment is called an amplification if ...References
[1] Fridlyand et al. Breast tumor copy number aberration
phenotypes and genomic instability, BMC Cancer, 2006.