Dear Melonnpan developer,
Thanks for providing the tool. I have installed the melonnpan in the R studio, and also downloaded the Github repository. However, I am very confused with the Melonnpan tutorial. Where should I find useful information to run the tool for testing the demo data? I checked other forum posts, but I was even more lost. Is it missing a lot of information because of the recent update? I have looked up in the manual GitHub - biobakery/melonnpan: Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles, and the tutorial melonnpan · biobakery/biobakery Wiki · GitHub. It seems we could run the analysis using both the command line and R, but I have no idea what commands should I use to run the tool. Where is the R script predict_metabolites.R? What’s is its function in R? What will be the input file? What will be a best practice I could do to run Melonnpan?
Looking forward to your reply. Thank you.
Cheng
Hi @Cheng_Guo - thanks for your interest in MelonnPan and apologies that you had trouble finding the instructions. On my end, I was able to follow the steps in the tutorial - could you please let me know which specific steps you are having trouble executing?
Thanks,
Himel
Hi Himel,
Thanks a lot for the prompt reply. I am using Mac with the R version of 4.1.1 (2021-08-10). Following the installation tutorial, I got errors as below. Could you please advise?
(base) chengguo [~/pipelines/Github]$ R -q -e “devtools::install_version(‘GenABEL.data’, version = ‘1.0.0’, repos = ‘http://cran.us.r-project.org’)”
devtools::install_version(‘GenABEL.data’, version = ‘1.0.0’, repos = ‘http://cran.us.r-project.org’)
Error in download_version_url(package, version, repos, type) :
couldn’t find package ‘GenABEL.data’
Calls: → → download_version_url
Execution halted
(base) chengguo [~/pipelines/Github]$ R -q -e “devtools::install_version(‘GenABEL’, version = ‘1.8-0’, repos = ‘http://cran.us.r-project.org’)”
devtools::install_version(‘GenABEL’, version = ‘1.8-0’, repos = ‘http://cran.us.r-project.org’)
Error in download_version_url(package, version, repos, type) :
couldn’t find package ‘GenABEL’
Calls: → → download_version_url
Execution halted
Also, I think for mac, the double-quote "’ is not allowed following the R command in the terminal, so I specifically convert all double-quote into the single-quote sign, and then it worked.
However, I was able to install the Melonnpan, GenABEL and GenABEL.data in the Rstudio, and I am more familiar with Rstudio. I would wonder if we have a tutorial with Rstudio?
Best,
Cheng
Hi Cheng - if you are in RStudio, you can find the relevant descriptions by typing ?melonnpan. train or ?melonnpan.predict in your R console. Note that, the command line versions of these two functions are: train_metabolites and predict_metabolites respectively, which the tutorial use for demonstration purposes but they should also work as R functions as well. Hope this helps!
Hi Himel
Thanks for the help! I am able to replicate the tutorial commands now.
Best,
CHENG