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Python code for running single file and multi-file LDA

License: GNU General Public License v3.0

Python 1.05% Jupyter Notebook 98.84% HTML 0.07% JavaScript 0.03%

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perdaug ymcdull mwang87 crystalxiao madeleineernst

lda's Issues

Check standards matches

Add function to make multifile dictionary, including adding names of individual files to the object for future reference

Change mzml names to accessions?

We had a problem with some data in which the mzml parser couldn't find the name 'mslevel' in one of the scans. The pymzml documentation says we can use either names or accessions. The accession for mslevel is:
MS:1000511
So we should perhaps change the loader to use this as I think this will always be present...

Should be a case of changing one line...

Add global topic index to the multifile object...

Add seed features into gnps / massbank / other? feature processing pipelines

urine, beer and combined notebooks don't propagate the filenames

Dictionaries

Manually add file names and topic index / metadata to run dictionaries.

Check topic metadata saved in dictionary.

Fix fixed_topic loading

At the moment, all pre-supplied fixed topics are loaded. There should be a filter, and only topics are kept if the total probability of the matched features exceeds some threshold.

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