PennParam: Constructor for class PennParam
Description
Parameters for the PennCNV Hidden Markov model
Usage
PennParam(states, referenceState = "222", prLessLikelyCN = 9e-04, prNonMendelian = 1.5e-06, prInitialStateNotDiploid = 4/5, prTransitionToNewState = 0.5, tauNM = 0.01)
"show"(object)
Arguments
states
character vector of possible trio states
referenceState
the reference (normal) trio copy number state (typically '222')
prLessLikelyCN
as defined in Wang et al. 2007, this is the probability of the less likely allele-specific copy numbers for the trio
prNonMendelian
the prior probability of a non-Mendelian copy number alteration
prInitialStateNotDiploid
initial probability for non-diploid states
prTransitionToNewState
probability of transitioning to a new state
tauNM
probability of transitioning from a Mendelian given previous event was non-Mendelian (and vice versa).
References
Wang et al., Genome Res. 2007 Nov;17(11):1665-74. PMID: 17921354