How to convert peak intensity to compound names

I used MetaboAnalystR package to process my raw data.
and the package output 2 csv files as “metaboanalyst_input.csv” and “annotated_peaklist.csv”
After getting these 2 files, I upload “metaboanalyst_input.csv” to MetaboAnalyst 5.0 website ----> statistical analysis(one factor) and output the OPLS-DA VIP results.

But I have problem with coverting the value to compound names
Is anyone know how to deal with it?

The statistical analysis modules do not perform any annotation - whatever ID types you upload are the ones displayed in the results.

Since you are already in R, I suggest using the ‘merge’ function to re-label your numerical peak IDs with the compound names. Then, if you analyze this labeled table in MetaboAnalyst, you will get the results with the compound names.

Thanks for your good advice.
But I can not find the “merge” function in metaboAnalystR package, is there any code available to map the peakIDs with the compound names?

merge() is a very common function in base R, so you do not need to load any special libraries to use it. Here is a tutorial on how to use it.

Thanks a lot! After I merge the data below, I got the file named “compound_db.qs”
annotated_peaklist.csv (1.4 MB)
metaboanalyst_input.csv (664.8 KB)

However, after searching many websites, I can’t find the way to process this file to do further analysis

You should search how to load a .qs file into R. There is a library for it.

It seems that you are not so comfortable using R - in this case, I suggest that you mainly use the web version of MetaboAnalyst, or take some introductory course to programming in R. There are many good tutorials online.