Joe Zhu issues

Results 55 issues of


                                            Joe Zhu

include pairwise IBD computation

Error prediction from the heterozygosity

make haplotype a separate class

compute wsaf within this class

mv updateReferencePanel from mcmc class to panel class

give options to generate output files, this is an issue in R version, as it generate output to files. let user to choose, add a flag

https://github.com/mcveanlab/DEploid-r/issues/41

enhancement

WARNINGS (Incomplete list)

Caveat flags for - Balanced proportion leads to high switch errors - Minor strain with low proportion leads to drop-out errors - Very imbalanced WSAF (contamination?) - Reference panel quality...

allow missing site in the reference strain

consider to use three states in the reference strain, 0, 1, and 2. where 2 is used for indicate missing, hence the emission should also include for missing state 2....

low priority

![image](https://github.com/insightsengineering/rlistings/assets/3692541/913234dc-fac9-4edc-b045-fdc80eb4d9ed) similar to the rtables cheatsheet, create one for tern, topics including * https://insightsengineering.github.io/tern/latest-tag/articles/missing_values.html * basic tabulation, https://insightsengineering.github.io/tern/latest-tag/articles/tables.html * https://insightsengineering.github.io/tern/latest-tag/articles/tern_formats.html * modeling * h_ functions * summarize functions

sme

Joe Zhu

inference result metrics

need to tidy up log file