callAmplifications.CBS: Calls (focal) amplifications

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

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.
verbose	Verbose.

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 ...

Author(s)

Henrik Bengtsson

References

[1] Fridlyand et al. Breast tumor copy number aberration phenotypes and genomic instability, BMC Cancer, 2006.

See Also

*callGainsAndLosses(). *callOutliers(). For more information see CBS.

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