search

baynec2 / mspms

R package for the analysis of Multiplex Substrate Profiling by Mass Spectrometry for Proteases (MSP-MS) Data
Other
0 stars 0 forks source link

motif analysis #3

Closed baynec2 closed 4 months ago

baynec2 commented 5 months ago

Check to see if there is some sort of open-source R solution to doing an IceLogo-like motif analysis.

It would be beneficial to make this work off of quantified values. Currently, the method just does some sort of enrichment analysis based on the motifs it was detected in compared to the background.

baynec2 commented 5 months ago

https://iomics.ugent.be/icelogoserver/resources/manual.pdf

^ can rewrite this in R and implement it in the package

baynec2 commented 5 months ago

added an implementation of this, but it appears to not give the exact same results. Had to multiply proportion by 10 instead of 100 to get the results to line up well, which I do not understand. Will do more work in the future and close when I am confident that the output matches that produced by IceLogo.

baynec2 commented 4 months ago

I fixed this. Now produces equivalent results to IceLogo