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cbielow / PTXQC

A Quality Control (QC) pipeline for Proteomics (PTX) results generated by MaxQuant
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QC metrics output as data frames #80

Open wyu opened 4 years ago

wyu commented 4 years ago

Is there a way to save the QC metric as data frames, in addition to the PDF/html report? We'd like to save them for longitudinal tracking purpose.

Wen

cbielow commented 4 years ago

this is coming up soonish. Until then, you can try to extract the data from the ggplot objects, which are stored in the list of metrics. You need to modify the package code for this, though

jw-houghton commented 3 years ago

Is there any update on this?

cbielow commented 3 years ago

I have started to implement mzQC output. The framework is ready, and there is currently one metric being exported. It should be easy now to export more data. Contributions welcome!

wyu commented 2 years ago

Very exciting to see the mzQC implementation! Are we limited by the vocabularies defined in the standard or we can put anything you have in PTXQC?

Thanks! Wen

cbielow commented 1 year ago

sorry, missed your question :/ Ideally, what we export is in the PSI-MS CV. If something is missing there, its very easy to add (just a PR, which is usually handled very quickly), or if you plan to use the mzQC in-house only, then you can use unofficial CV's as well.

cbielow commented 1 year ago

There is a grant application running ATM, which will hopefully allow us to implement the full set of metrics for mzQC. Fingers crossed. (and contributions still welcome :))