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stanstrup / PredRet

Shiny app for retention time prediction
GNU General Public License v2.0
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How to run the PredRet within R? #81

Closed Danissss closed 4 years ago

Danissss commented 4 years ago

Could you provide any sample run command and the result?

stanstrup commented 4 years ago

Depends what you want to do. With the package you can pull information from the database. But not, for example, add data or do the modeling.

See here for just getting data: http://stanstrup.github.io/annotate_with_PredRet.html PredRet_get_chrom_systems can be used to see what systems are in the database.

Danissss commented 4 years ago

Thanks!

Danissss commented 4 years ago

Hi, Sorry, I was confused. After I installed everything

install.packages("devtools")
library(devtools)

source("https://bioconductor.org/biocLite.R")
biocLite("pcaMethods")

install_github("mongosoup/rmongodb")
install_github("stanstrup/Rplot.extra")
install_github("stanstrup/massageR")

install_github("stanstrup/PredRet",subdir = "PredRetR")

How should I achieve Retention Time Prediction (from your paper) procedure using R instead of using web interface?

I have list of inchi (rt may not be available for every compounds).

Thank you!

stanstrup commented 4 years ago

You cannot. Sorry. You have to use the web interface. You can only download data (and predictions) from R. You cannot add data to the system.

Danissss commented 4 years ago

Yes, I only want to do predictions from R. I am not going to add data to system.

stanstrup commented 4 years ago

The system doesn't work like that. You cannot make predictions for a system if data has not been uploaded for that system. You can download existing predictions from R. But not "make" predictions.