PSCBS (version 0.63.0)

callSegmentationOutliers: 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

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

See Also

Internally smooth.CNA is utilized to identify the outliers.