Addition of method to filter features based on quality assessment #713
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jorainer
requested changes
Jan 25, 2024
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Really great PR adding relevant functionality @philouail ! I have some change requests, but only minor ones.
philouail
commented
Jan 26, 2024
R/method-filterFeatures.R
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| #' ## Set up parameter to flag possible contaminant based on blank samples | ||
| #' filter <- BlankFlag( | ||
| #' qcIndex = sampleData(test_xcms)$sample_type == "QC", | ||
| #' blankIndex = sampleData(test_xcms)$sample_type == "study") |
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here i'm not sure what to do, I think it might be confusing for people that i use study samples as blank samples(because the object does not have blanks). I can explain it but is it a good idea ?
Otherwise should I had like 2 randomly generated blank sample to the object and use that as an example ?
jorainer
approved these changes
Jan 29, 2024
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Great contribution @philouail ! I have only very minor things/typos left. After that I would be OK for merging - given @sneumann agrees.
sneumann
approved these changes
Feb 1, 2024
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Here is the implementation of the
filterFeaturesfunction with different quality assessment methods. I also wrote the method so that they can handle bothXcmsResultobjects andSummarisedExperimentobjects.@jorainer I have updated the
PercentMissingFilterso that now it filters based on the different sample types usingfactor.I tried to make the documentation comprehensive but don't hesitate to tell me if something is not clear or not explained in enough details for the users.
These different classes/methods are based on the quality assessment function from MetaboCoreUtils. So some information can also be found in this package.
Thanks in advance for the feedback !