Arguments
mu0
a vetor of the same length as number of positions: the initial value of position effect mu.
delta0
a vetor of the same length as number of samples: the initial value of sample effect delta.
zm1
the output of estep: the posterior probabilities of genotype RR for n samples at m positions
z0
the output of estep: the posterior probabilities of genotype RV for n samples at m positions
zp1
the output of estep: the posterior probabilities of genotype VV for n samples at m positions
dat
a n*m matrix: the ith row, jth column of the matrix represents the non-reference counts of ith sample at jth position.
cvg
a n*m matrix: the ith row, jth column of the matrix represents the depth of ith sample at jth position.
eps
a single value: a threshold to control the convergence criterion. The default is 1e-06.