PennParam {MinimumDistance} | R Documentation |
PennParam
Parameters for the PennCNV Hidden Markov model
PennParam(states, referenceState = "222", prLessLikelyCN = 9e-04, prNonMendelian = 1.5e-06, prInitialStateNotDiploid = 4/5, prTransitionToNewState = 0.5, tauNM = 0.01) ## S4 method for signature 'PennParam' show(object)
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). |
object |
a |
Wang et al., Genome Res. 2007 Nov;17(11):1665-74. PMID: 17921354