callOutliers.CBS: Calls outliers

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

Calls outliers

Description

Calls outliers.

Usage

## S3 method for class 'CBS'
callOutliers(fit, adjust=1, method=c("ucsf-mad"), ...)

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.
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 columns 'negOutlierCall' and 'posOutlierCall' have been appended to the segmentation table.

The UCSF 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.]

Author(s)

Henrik Bengtsson

References

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

See Also

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

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