callSegmentationOutliers: Calls/drops single-locus outliers along the genome

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

Calls/drops single-locus outliers along the genome

Description

Calls/drops single-locus outliers along the genome that have a signal that differ significantly from the neighboring loci.

Usage

 ## Default S3 method:
callSegmentationOutliers(y, chromosome=0, x=NULL, method="DNAcopy::smooth.CNA", ...,
  verbose=FALSE)
 ## S3 method for class 'data.frame'
callSegmentationOutliers(y, ...)
 ## Default S3 method:
dropSegmentationOutliers(y, ...)
 ## S3 method for class 'data.frame'
dropSegmentationOutliers(y, ...)

Arguments

y	A numeric vector of J genomic signals to be segmented.
chromosome	(Optional) An integer scalar (or a vector of length J contain a unique value). Only used for annotation purposes.
x	Optional numeric vector of J genomic locations. If NULL, index locations 1:J are used.
method	A character string specifying the method used for calling outliers.
...	Additional arguments passed to internal outlier detection method.
verbose	See Verbose.

Value

callSegmentationOutliers() returns a logical vector of length J. dropSegmentationOutliers() returns an object of the same type as argument y, where the signals for which outliers were called have been set to NA.

Missing and non-finite values

Signals as well as genomic positions may contain missing values, i.e. NAs or NaNs. By definition, these cannot be outliers.

Author(s)

Henrik Bengtsson

See Also

Internally smooth.CNA is utilized to identify the outliers.

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