forward_backward_: forward_backward_

In stephenbates19/digitaltwins: Causal inference for SNPs

Description

Carry out the forward-backward algorithm for the HMM implied by knowing the two parental haplotypes.

Usage

forward_backward_(x, p1, p2, d, p, lambda, epsilon, start, end)

Arguments

x	0-1 vector of length p giving the offspring haplotypes
p1	0-1 vector of length p giving one parental haplotype
p2	0-1 vector of length p giving the other parental haplotype
d	numberic vector of length p - 1 giving the distance between each site
p	length of the vector x
lambda	the recombination rate, a multiplier for the distance d
epsilon	the pointwise mutation rate
start	indexes of the subset of x to perform the computation (1 indexed)
end	indexes of the subset of x to perform the computation (1 indexed)

Value

p1_start: the probability that the latent state immediately before the specified window is 1, i.e. the offspring is being copied from p1.

p1_start_odd: probability of an odd number of recombinations given that the latent state immediately before the specified window is 1.

p2_start_odd: probability of an odd number of recombinations given that the latent state immediately before the specified window is 2.

stephenbates19/digitaltwins documentation built on Feb. 25, 2020, 12:41 a.m.