This would add a per-sample filter code in the event that any two replicate MCMC traces have high support for differing phenotypes.
A threshold parameter for the filter with a sensible default e.g. 60% posterior probability support for in congruent phenotypes.
This filter is unlikely to filter anything that is not filtered by the posterior probability filter (unless number of chains >= 10) however it is useful for downstream analysis of why a given locus/sample is not assembling.
This would require calculating a per chain posterior distribution and checking that the mode phenotypes from each posterior that exceed the specified threshold support are identical.
The code for this filter could be ci<theshold> defaulting to ci60 "Chain incongruence with 60% posterior support".
timothymillar
commented
3 years ago
This would add a per-sample filter code in the event that any two replicate MCMC traces have high support for differing phenotypes. A threshold parameter for the filter with a sensible default e.g. 60% posterior probability support for in congruent phenotypes. This filter is unlikely to filter anything that is not filtered by the posterior probability filter (unless number of chains >= 10) however it is useful for downstream analysis of why a given locus/sample is not assembling.
This would require calculating a per chain posterior distribution and checking that the mode phenotypes from each posterior that exceed the specified threshold support are identical. The code for this filter could be
ci<theshold>defaulting toci60"Chain incongruence with 60% posterior support".