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saezlab / MetaProViz

R-package to perform metabolomics pre-processing, differential metabolite analysis, metabolite clustering and custom visualisations.
https://saezlab.github.io/MetaProViz/
GNU General Public License v3.0
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Preprocessing Syntax #47

Closed dprymidis closed 1 year ago

dprymidis commented 1 year ago
  1. Rename Experimental_design to InputSettingsFile
  2. add InputSettingsInfo = c(UniqueID = "Sample_ID" (rownames), Condtions= "Conditions, Biological_Replicates = "Biol_rep"...)
  3. rename blank samples to media for CoRe
  4. add a parameter in InputSettingInfo c(CoRe_media = "Name_of_media_samples")
  5. Do the checks and if something is passed and is missing give warnings etc.
dprymidis commented 1 year ago

This is Done! I updated the vignettes and the function for preprocessing (for CoRe) runs like this:

image

Notes:

  1. I did not use the UniqueID = "Sample_ID" (rownames), as I thought that the "same rownames" syntax in used in all the scripts so far, and not all function have the Plot_settingsInfo ( I have to checkthis). Also, it seems easier to me for someone to know that samples go to rownames in all cases than having one function where you have to spesify the sample ID. On the other hand, we can change that everywhere where applicable. Any thoughts?

  2. The syntax of DMA has to also change and I will do that along with adding the ANOVA.

ChristinaSchmidt1 commented 1 year ago
  1. Yes I agree. I also updated this last week for the PCA plot as I noticed that it still uses the column uniqueID. In general lets aim to always have the uniqueIDs (=unique sample identifiers) as rownames and if the user provides Plot_SettingFile this also needs to have the UniqueIDs as rownames.
  2. That makes sense with what we discussed. You can write down the comments or changes for DMA into the issue. Once you have made the changes to DMA, you can also change the section in the vignette accordingly :)

Thanks a lot for this and its really nice that you updated the vignette too!

dprymidis commented 1 year ago

This is done!

ChristinaSchmidt1 commented 1 year ago

Ok, then I will close the issue.