8000 Feat: Auto QC calculations by dmccloskey · Pull Request #4637 · OpenMS/OpenMS · GitHub
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Feat: Auto QC calculations #4637

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Merged
merged 33 commits into from
Apr 30, 2020
Merged

Feat: Auto QC calculations #4637

merged 33 commits into from
Apr 30, 2020

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dmccloskey
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New features

  • automated estimation of default QC filter/flagging values
  • ability to filter based off of %RSD values as calculated by e.g., pooled QCs or replicate Samples
  • ability to filter based off of %BackgroundInterference values as calculated by e.g., Blank samples
  • store method for the MRMFeatureQC class

Code changes

  • removed old code around potential QCML support
  • comparison methods for MRFeatureQC

dmccloskey added 25 commits April 11, 2020 10:53
@dmccloskey
fix: small cleanup of MRMFeatureQC header/cpp files
ba4a57e
@dmccloskey
feat: added new members to MRMFeatureQC in preparation for new method…
57da84b 
…s to filter on new members in MRMFeatureFilter
@dmccloskey
fix: removed potential future QCML features as there appears to be no…
b0d9902 
… interest in moving in supporting QCML with MRMFeatureFilter
@dmccloskey
fix, feat, doc: removed previously added members to MRMFeatureQC as t…
f37f72d 
…hey were not needed and introduced docstrings and method signatures to MRMFeatureFilter
@dmccloskey
feat: EstimateDefaultMRMFeatureQCValues without tests
6e8181b
@dmccloskey
tests: tests for helper methods updateRange and updateMetaValue
b8732c6
@dmccloskey
feat: TransferLLoQandULOQToCalcConcBounds without tests
2b16be6
@dmccloskey
fix: failing build/tests
1c4d043
@dmccloskey
WIP: EstimatePercRSD; todo: refactor into smaller methods that can ea…
999c2a6 
…ch be unit tests
@dmccloskey
feat: EstimatePercRSD with submethods without unit tests
ed22cc8
@dmccloskey
feat: EstimateBAckgroundInterferences without unit tests
d77d33c
@dmccloskey
tests: setMetaValue
08802f1
@dmccloskey
tests: zeroFilterValues
aab3d7c
@dmccloskey
fix, tests: calculateFilterValuesMean
cbb8670
@dmccloskey
fix, tests: calculateFilterValuesVar and calculateFilterValuesPercRSD
f33224a
@dmccloskey
WIP: EstimateBackgroundInterferences test
9b51739
@dmccloskey
WIP: accumulateFilterValues test
af092b8
@dmccloskey
tests: accumulateFilterValues
183aabd
@dmccloskey
fix, tests: changed the behavior of EstimateDefaultQCs so that the mi…
b3ced34 
…nimum and maximum ranges are determined by the samples and not the template. Will also add a parameter to the arguments to allow for updating instead of overwritting
@dmccloskey
feat, tests: options for how to estimateDefaultQCValues and associate…
099f230 
…d tests
@dmccloskey
feat, tests: FilterFeatureMapPercRSD
3733054
@dmccloskey
feat, test: filterFeatureMapBackgroundIntensity
1f8f1db
@dmccloskey
feat: MRMFeatureQCFile::store without unit tests
2856eeb
@dmccloskey
wip: adding in comparators to structs in MRMFeatureQC
226be3f
@dmccloskey
fix, tests: added comparator to MRMFeatureQC, fixed a few bugs in sto…
d8baf25 
…re, and added tests for MRMFeatureQCFile::store
@ghost
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ghost commented Apr 13, 2020 •
edited by ghost
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@dmccloskey
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The CI failures appear to be due to the lint checks add a test that appears quite unrelated to the PR on windows. Please let me know how best to proceed.

@jpfeuffer
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Correct, the test is unrelated. But could you try to address the linting errors quickly?
http://cdash.openms.de/viewTest.php?onlyfailed&buildid=432435

And you seem to have pulled over changes to the referenced version of the contribs from another branch or so. Can you try to revert that part?
Potentially with
git submodule --init contrib

@dmccloskey
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Please let me know if something is still up with the submodules. I am not sure what happened exactly to cause the changes. I reverted them using git submodule init contrib.

cbielow
cbielow reviewed Apr 15, 2020
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cbielow
cbielow reviewed Apr 15, 2020
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cbielow
cbielow reviewed Apr 15, 2020
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cbielow
cbielow reviewed Apr 15, 2020
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cbielow
cbielow reviewed Apr 15, 2020
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@timosachsenberg
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@cbielow is there some overlap to your QC approach or something we could consider in the future to harmonize QC approaches?

@dmccloskey
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I wanted to check in to see if this branch is ready to be merged.

cbielow
cbielow reviewed Apr 21, 2020
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@cbielow
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cbielow commented Apr 21, 2020

@cbielow is there some overlap to your QC approach or something we could consider in the future to harmonize QC approaches?

if this is for MRM data, there is probably not a lot of overlap. Nevertheless, computation of QC might be extracted into a separate class and put into /src/QC/, just for clearer interfaces??

@cbielow
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cbielow commented Apr 21, 2020

looks good.
Maybe have a look at the codefactor warnings. Some of them seem easy to fix.

@dmccloskey
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Please advice on the appleclang failure.

@jpfeuffer
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Unrelated. Wanna merge?

@dmccloskey
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Yes

@timosachsenberg timosachsenberg merged commit 7aa1f75 into OpenMS:develop Apr 30, 2020
@dmccloskey dmccloskey deleted the feat/autoQC branch August 21, 2020 12:10
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4 participants
@dmccloskey @jpfeuffer @timosachsenberg @cbielow
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