PennParam: Constructor for class 'PennParam'

Description Usage Arguments References

View source: R/methods-PennParam.R

Description

Parameters for the PennCNV Hidden Markov model

Usage

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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


rscharpf/MinimumDistance documentation built on Sept. 16, 2019, 4:12 a.m.