updog_mcmc: The updog Gibbs sampler to jointly estimate the parental and...
In dcgerard/updogAlpha: Using Parental Data for Offspring Genotyping

The updog Gibbs sampler to jointly estimate the parental and offspring genotypes.

1 2	updog_mcmc(ocounts, osize, qarray, r1vec, r2vec, seq_error = 0.01, itermax = 1000, burnin = 250)

`ocounts`	A vector of non-negative integers. The ith element is the number of reads of the reference allele in the ith child.
`osize`	A vector of positive integers. The ith element is the total number of reads for the ith child.
`qarray`	An array of proportions. Each dimension size is equal to the ploidy plus 1.
`r1vec`	The posterior probabilities of the genotypes of parent 1 conditional only on the sequence data from parent 1.
`r2vec`	The posterior probabilities of the genotypes of parent 2 conditional only on the sequence data from parent 2.
`seq_error`	A non-negative numeric. This is the known sequencing error rate. The default is to estimate this using data that are all approximately the reference allele.
`itermax`	The maximum number of iterations to run the Gibbs sampler.
`burnin`	The number of iterations to skip.