Example usage with non-packaged data #31
Replies: 4 comments 4 replies
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Dear Fabian, please do have a look here: There is an example of reading a "combined_protein.tsv". There is also an example of reading MSFragger data here: Hope this helps. |
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Thank you for the links. That's indeed very helpful. It seems that there are functions that are not showing up in the manual: https://rdrr.io/github/wolski/prolfqua/man/ There are many documented |
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Also, I find it a bit strange to see in the following line in the Example of MSFragger because this might imply that the data used is from MaxQuant instead of MSFragger. Also, the linked docs above are reached by clicking MSFragger in the main documentation website, but then there is no function MSFragger, but a couple of functions with different names. Maybe this is just the way R documentation works, but this is somewhat confusing for me. I am also kind of expecting that there must be a function named I hope this feedback helps to improve the docs and maybe even the function names. |
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Thanks for the comments. Yes, 16 refers to version 1.6 of Fragpipe, actually IonQuant, AFAIK, and not just MSFragger. However, the functions should show up in the help; they are not internal: I will update the names of the functions and the documentation for the package's next release (maybe try to autodetect the version of fragpipe used) and then close the ticket.
Thanks again. Feedback welcome. |
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Thank you for the clarifications. I see now, my lack of experience searching for R documentation is also partially to blame. The functions show up in the Functions section of the documentation, but not in the list of Man pages. The MaxQuant equivalent, however, do. I was using FragPipe version 17.1. It would be great to be able to use prolfqua with these searches. |
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I am sure you can use tidy_MSFragger_combined_protein_V16 with 1.7.1 combined_protein.tsv |
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Thank you! |
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Hi Fabian, I created a new release Where I did rename the functions tidy_MSFragger.. to tidy_FragPipe.. https://fgcz.github.io/prolfqua/reference/FragPipe.html The read combined_protein functions for older versions of fragpipe are now called: All the |
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I was looking for the right way to read in MSFragger search results and didn't really find a nice example in the tutorials that showed how to read in such data. Did I just not find it, or is this indeed missing from the documentation/tutorials?
I think a section in the docs that explains how to read in data and examples for all the popular search engines would be really nice.
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