Description Usage Arguments See Also
View source: R/methodsMinDistParam.R
The MinDistParam
class contains parameters used for the
segmentation implemented in the DNAcopy
package, parameters
extracted from the PennCNV
HMM such as parentoffspring
transmission parobabilities (see citation below), and initial
values / parameters for computing emission probabilities.
1 2  MinDistParam(nMAD = 0.75, dnacopy = DNAcopyParam(),
penncnv = PennParam(), emission = EmissionParam(), thin = 10L)

nMAD 
a lengthone numeric vector indicating the minimal number of median absolute deviations of the mean segmented minimum distance from zero. For nonzero segments (# median absolute deviations > nMAD), maximum a posteriori estimates of the parentoffspring copy number states are computed. Segments with minimum distance values near zero are not called as they are less likely to correspond to regions with de novo copy number alterations. 
dnacopy 
an object of class 
penncnv 
probabilities/parameters of the PennCNV hidden Markov model 
emission 
an object of class 
thin 
a lengthone vector indicating whether to thin the
data. This is primarily for internal use in conjunction with the

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