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dcgerard / updog

Flexible Genotyping of Polyploids using Next Generation Sequencing Data
https://dcgerard.github.io/updog/
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Is mupdog available for half-sib families? #18

Open LizPopowski opened 3 years ago

LizPopowski commented 3 years ago

Hi, I have read about mupdog for use with half-sib families. This is package currently available? I found a reference to it at https://mran.microsoft.com/snapshot/2018-07-16/web/packages/updog/readme/README.html but I'm not able to locate any other references to processing half-sib families.

Also, what is the most recent version of updog available?

Thanks, Liz

dcgerard commented 3 years ago

Hey @LizPopowski,

Thanks for trying out the updog package!

mupdog() was always experimental. And since it was slow and I never got around to testing it extensively, I ultimately removed it from the package.

You can try it out if you are interested by installing an older version of updog:

library(remotes)
remotes::install_version(package = "updog", version = "1.2.0", repos = "http://cran.us.r-project.org")

Using multidog() with model = "norm" would not be incorrect --- the assumptions of that model are fulfilled, it just does not take advantage of the pedigree information.

The most recent CRAN version is 2.0.2, while the dev version on GitHub is 2.1.0. The dev version uses the future package so that folks have more control over the parallelization, but I haven't pushed it to CRAN yet because I've heard some folks are having trouble with the future package.