search

qiime2 / q2-longitudinal

QIIME 2 plugin for paired sample comparisons
BSD 3-Clause "New" or "Revised" License
9 stars 18 forks source link

feature volatility pipeline #95

Closed nbokulich closed 5 years ago

nbokulich commented 6 years ago

fixes #93

~Depends on https://github.com/qiime2/q2-sample-classifier/pull/91~ ~Depends on https://github.com/qiime2/q2-sample-classifier/pull/98~ ~Depends on https://github.com/qiime2/q2-sample-classifier/pull/116~ ~Depends on https://github.com/qiime2/q2-sample-classifier/pull/120~

~Also need to:~ ~1. resolve metadata transformer error~ ~2. add tests~ ~3. switch from NCV to CV with feature selection. Remove prediction results from output?~ ~4. validate metadata: state_column must be numeric~ ~5. volatility sorts features by name! not the actual order in the metadata (sorted by importance). Need to either (a) make volatility sort features by importance or (b) do #94~

DO NOT MERGE — blocked by pending PR to port sample-classifier type/format registrations to q2-types.

thermokarst commented 6 years ago

@nbokulich - now that https://github.com/qiime2/q2-sample-classifier/pull/91 is in, is it safe to drop the "DO NOT MERGE" label?

nbokulich commented 6 years ago

thx for the ping @thermokarst . Not yet — See the outstanding item on the to-do list.

You are welcome to review if you'd like — I am hoping we can get CV in place soon — but we are squeaking close to the deadline, so this may not make it in time for this release. 😞