ocbe-uio / rBAPS

R implementation of the BAPS software for Bayesian Analysis of Population Structure
http://www.helsinki.fi/bsg/software/BAPS/
GNU General Public License v3.0
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Complete greedyMix features #24

Open wleoncio opened 2 years ago

wleoncio commented 2 years ago

The function currently loads the raw data, but doesn't process it. Check the code in greedyPopMix() and the original MATLAB code to see what else needs to be done (e.g. call handleData()).

To close the issue, make sure greedyMix() works for the following formats:

wleoncio commented 7 months ago

Implemented rest of algo, which got us back to the issue of an endless loop. Investigating indMix(), closely comparing its output with the one on the original BAPS...

wleoncio commented 1 month ago

Done for all originally-supported formats, namely BAPS and GenePop. VCF and BAM are not on the original code, so one needs to reshape them into a format the rest of the function can use. For FASTA, a function was created to convert it to BAPS. It's still broken, but might be the easiest way to go here.