polyfreqs_pps: Posterior predictive model checks for polyfreqs
In polyfreqs: Bayesian Population Genomics in Autopolyploids

Description Usage Arguments Details Value References

Uses the posterior distribution of allele frequences from a polyfreqs run to test model fit using the posterior predictive model checking procedure described in Blischak et al.

1	polyfreqs_pps(p_post, tM, rM, ploidy, error)

`p_post`	A matrix containing the posterior samples from a `polyfreqs` run.
`tM`	Total reads matrix: matrix containing the total number of reads mapping to each locus for each individual.
`rM`	Reference reads marix: matrix containing the number of reference reads mapping to each locus for each individual.
`ploidy`	Ploidy level of individuals in the population.
`error`	The level of sequencing error. A fixed constant.

The observed read count ratio (r/t) for each locus is summed across individuals and then compared to a distribution of read ratios simulated using the posterior allele frequencies by taking their difference. The criterion for passing/failing the posterior predictive check is then made on a per locus basis based on whether or not the distribution of read ratio differences contains 0 in the 95

A list with two items:

ratio_diff: The posterior predictive samples of the difference between the simulated read ratios and the observed read ratio summed across individuals at each locus.
locus_fit: A logical vector indicating whether or not each locus passed or failed the posterior predictive model check.

Blischak PD, LS Kubatko and AD Wolfe. Accounting for genotype uncertainty in the estimation of allele frequencies in autopolyploids. In revision.

polyfreqs documentation built on May 2, 2019, 9:28 a.m.