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mgalardini / pyseer

SEER, reimplemented in python 🐍🔮
http://pyseer.readthedocs.io
Apache License 2.0
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Add a script to compute a covariance matrix from unitigs presence/absence #206

Closed mgalardini closed 2 years ago

mgalardini commented 2 years ago

A reviewer for our last paper suggested to compute the LMM Kinship matrix from unitigs presence/absence patterns, so that core/accessory population structure is fully account for. Could this be useful as part of pyseer's scripts? We have it here for the moment: https://github.com/microbial-pangenomes-lab/2021_ecoli_pathogenicity/blob/main/workflow/scripts/unitigs2covar.py

johnlees commented 2 years ago

Yeah could certainly add this! It's also possible in fastlmm to use two kinship matrices, that might be another way of doing it

mgalardini commented 2 years ago

Closing this as we actually have this script already! See PR #211 for some fixes to it