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ByrumLab / proteoDA

GNU General Public License v3.0
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Deprecate or remove filter_protein_contaminants #173

Closed tjthurman closed 1 year ago

tjthurman commented 1 year ago

This is an UAMS-only function anyway. I created it to make our functions more functionally pure (that is, make the data import only do data importing, and not do other stuff). But, with the new uniprot_column requirements (see #172), we need to filter out contaminants before we create the DAList object, as contaminants have the same uniprot ID and make it so we can't use uniprot IDs as rownames.

Now that we filter out contaminants in read_DIA_data again, filter_protein_contaminants is no longer needed.

jbird9 commented 1 year ago

So should we just delete the function from the program or just move it to the internal functions?

tjthurman commented 1 year ago

For the public version of the package (this repo), we should just delete it after we split the package into private and public. I think we could keep it for the internal version of the package if we want, though it will be a little redundant.