smoothSnp {SNPchip} | R Documentation |
A loess smoother for finding regions of reduced copy number and loss of heterozygosity.
smoothSnp(object, ...)
object |
Object derived from AnnotatedSnpSet |
... |
For additional arguments see details. |
Additional arguments include the chromosomes (character vector) and samples (numerical vector) to smooth. Options for smoothing are set by specifying the span and the method. See the SNPchip vignette.
See the R package VanillaICE for a hidden Markov model for more formal inference regarding regions of LOH and copy number alterations.
An object of the same class, e.g., AnnotatedSnpSet
, where
assayData elements copyNumber and calls are replaced by the smoothed
values.
Robert Scharpf
RS