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matsengrp / sumrep

Summary statistics for repertoires
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Standardize locus input #30

Open BrandenOlson opened 5 years ago

BrandenOlson commented 5 years ago

Functionality across sumrep is dependent on which locus the repertoire comes from, and this information is input differently across functions. We will standardize this so that, when locus is important, the function will have a locus argument which expects one of "tra", "trb", "trd", "trg", "igl", "igk", or "igh". This is already implemented in getPartisAnnotations and getIgBlastAnnotations, but compareRepertoires asks for a receptor_type and chain_type separately. I'll look for other cases to standardize as well.

I'll note that there is already a checkForValidLocus function which checks that the locus argument matches one of the above options.

BrandenOlson commented 5 years ago

This has been incorporated into IGoR, compareRepertoires, and in the model validation example scripts.