Can not find the file "metaboanalyst_input.csv

MetaboAnalyst
,
1 
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.
2

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.

3

Hi Jess,
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.

4

Hi Jess,
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.

5

Ok, I talked to the person who maintains this package/tutorial and they should respond shortly! Thanks for bringing this to our attention.

6

Hi Chenx,

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)

Bests,
Zhiqiang

7

Thanks for your help