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morinlab / GAMBLR

Set of standardized functions to operate with genomic data
MIT License
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COMPOSITE class as default is a bug #54

Closed rdmorin closed 2 years ago

rdmorin commented 2 years ago

There's a bug in get_gambl_metadata that causes any case without a LymphGen class to be assigned as COMPOSITE. This should be changed to either set them to "Other" or, better yet, a class that isn't part of LymphGen but also doesn't imply a composite class.

lkhilton commented 2 years ago

This code probably also needs to be updated to use the published lymphgen when no locally-generated calls are available so that the DLC cases can be labeled.

rdmorin commented 2 years ago

The ideal fix will be to add a new collate_ function (e.g. collate_lymphgen) and have it do the work instead of doing this in the metadata function. We can use NA for any case that doesn't have a lymphgen class but should also draw from all sources of lymphgen as noted by Laura.

Kdreval commented 2 years ago

This has now been addressed in PR #63 , including the new collate_lymphgen function.