I am trying to run MelonnPan Predict on my previous trained model, however I have encountered some problem as I intend to explain below.
- First , I have paired 16S RNA data (out) with KO data (from PICRUST), with this two datasets I normalized and filtered my metag and metab inputs before running MelonnPan_Train command as indicated below.
melonnpan::melonnpan.train(metab= “C:/Users/Sandra.Diaz/Desktop/MelonnPan/metag_input2.csv”, metag = “C:/Users/Sandra.Diaz/Desktop/MelonnPan/metab_input2.csv”, outputDirectory = “C:/Users/Sandra.Diaz/Desktop/MelonnPan/”)
- Once my data is trained, I run MelonnPan predict, by using the three inputs needed as indicated in the command below.
mp.predict ← melonnpan.predict(metag=(“C:/Users/Sandra.Diaz/Desktop/Example2/metag_inputE.coli2.csv”), weight.matrix=(“C:/Users/Sandra.Diaz/Desktop/Example2/MelonnPan_Trained_Weights.csv”), train.metag=(“C:/Users/Sandra.Diaz/Desktop/Example2/metag_input2.csv”) , criticalpoint = 0.9793, corr.method=“pearson”, output= “C:/Users/Sandra.Diaz/Desktop/Example2/”)
However I am getting this error:
Error in ztransform(formula, data, family) :
formula argument must be a formula or one of (numeric, integer, double)
Además: Warning message:
In data.table::fread(Input, header = FALSE) :
Stopped early on line 3. Expected 2040 fields but found 2063. Consider fill=TRUE and comment.char=. First discarded non-empty line: <<otu_001,0,0,0,0,0,0,0,0,-2,93E+09,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,-4,
I checked all the data sets and filter them again in case that was the issue however I cannot find what is going on, I am probably missing something in the workflow, so I would appreciate any kind of advice with it.
Thanks a lot,