Dear Developer, Thank you for developing the amazing tool, I am try the example data in R, when I run the following function, I did not find csv file in my folder. mSet<-Read.TextData(mSet, "metaboanalyst_input.csv", "colu", "disc") Based on my understanding, it should be generated by the above function "maPeaks <- FormatPeakList(annotPeaks, annParams, filtIso =F, filtAdducts = FALSE, missPercent = 1)" but I did not find it at all in my folder. Any idea on this issue? Thanks.
Can you try the command to find the current working directory in R: getwd()
The function should output files here. It may be creating them in a different place than you expect.
Thank you for your reply. Actually, I check the folder I am working on. However, I did not find it.
What I should do? Thanks.
Please check the tutorial of MetaboAnalystR, seems you missed one function to export the information to “metaboanalyst_input.csv”, and FormatPeakList() can not generate this file.
Ok, I talked to the person who maintains this package/tutorial and they should respond shortly! Thanks for bringing this to our attention.
Thanks for your question. You need one more step to generate the csv file. Please use this following command to make it.
mSet <- FormatPeakList(mSet = mSet, annParams, filtIso =F, filtAdducts = FALSE,missPercent = 1) write.csv(mSet@dataSet, file = "metaboanalyst_input.csv",row.names = F)
Thanks for your help