callSegmentationOutliers {PSCBS} | R Documentation |
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 |
|
chromosome |
(Optional) An |
x |
Optional |
method |
A |
... |
Additional arguments passed to internal outlier detection method. |
verbose |
See |
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. NA
s or NaN
s. By definition, these cannot
be outliers.
Author(s)
Henrik Bengtsson
See Also
Internally smooth.CNA
is utilized to identify
the outliers.