Description Usage Arguments Value
Marginalizes out the hidden variables X using the forward algorithm to compute the likelihood of an observed sequence of emissions.
1 2 |
Y |
observed sequence of emissions (1: heterozygous site; 0: homozygous site). |
M |
size of hidden statespace; an integer. |
rho |
the recombinartion rate between two ajacent sites. |
theta |
mutation rate between two sequences at any given position. |
Px |
transition kernel of hidden variables. May be passed instead of rho. |
mu |
a vector of emission probabilities. The ith entry is interpreted as the probability of Y=1 given X=i. May be passed instead of theta |
x0_prior |
initial distribution of the hidden markov chain. Defaults to a uniform distribution. |
a single number, corresponding to L(theta,rho|Y)
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