How to remove NAs from mset object in MetaboAnalystR

Question

[lewhiteside]

I am trying to perform pathway analysis with MetaboAnalystR,

I have performed the t-tests:

> mSet<-Ttests.Anal(mSet, F, 0.25, FALSE, TRUE)
[1] "A total of 43 significant features were found."

However when I try to convert it to the input for mummichog I am getting the following warning:

Convert2Mummichog(mSet, rt = TRUE)
Warning message:
In Convert2Mummichog(mSet, rt = TRUE) : NAs introduced by coercion

Then, I get the following error:

> SetPeakFormat("mpt")
> mSet<-UpdateInstrumentParameters(mSet, "5", "negative");
[1] "Mass accuracy must be numeric!"
> mSet<-Read.PeakListData(mSet, "mummichog_input_2021-02-18.txt");
[1] "mprt"
> mSet<-SanityCheckMummichogData(mSet)
[1] "NA values found in the uploaded data!"

Is anyone able to help me with this I cant find any solutions!

Thank you!