PennParam: Constructor for class 'PennParam'

In MinimumDistance: A Package for De Novo CNV Detection in Case-Parent Trios

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
)

## S4 method for signature 'PennParam'
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).
object	a PennParam object

References

Wang et al., Genome Res. 2007 Nov;17(11):1665-74. PMID: 17921354

MinimumDistance documentation built on Nov. 8, 2020, 11:11 p.m.