TransitionParam: Constructor for TransitionParam class

In VanillaICE: A Hidden Markov Model for high throughput genotyping arrays

Description

Contains parameters for computing transition probabilities

Usage

TransitionParam(taup = 1e+10, taumax = 1 - 5e+06)

## S4 method for signature 'TransitionParam'
show(object)

Arguments

taup	length-one numeric vector
taumax	The maximum probability that the current state is the same as the preceding state. See details
object	a TransitionParam object

Details

Diagonal elements of the transition probability matrix are computed as e^-2*d/taup, where d is the distance between markers i and i-1 and taup is typically in the range of 1xe10. This probability is constrained to be no larger than taumax. The probabilities on the off-diagonal elements are the same and are subject to the constraint that the rows of the transition probability matrix sum to 1.

Examples

TransitionParam()
## higher values of taup make transitions between states less likely
TransitionParam(taup=1e12)

VanillaICE documentation built on Nov. 8, 2020, 7:33 p.m.