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, ...)

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.

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.

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