This package consist of four functions viz. "drug.class.deterministic", "drug.class.stochastic", "drug.resistome.deterministic" and "drug.resistome.stochastic" respectively to predict resistome of Escherichia coli and Pseudomonas aeruginosa for drug chemical structure.
It predicts the class/family of unknown candidate drug molecule using two algorithms viz. deterministic model ("drug.class.deterministic") and stochastic model ("drug.class.stochastic") [Unpublished data]. Furthermore once the drug class is predicted, the resistome of the predicted drug class can be fetched out from database using "drug.resistome.deterministic" and "drug.resistome.resistome" functions.
- R (tested in version 3.4.3)
- ChemmineR (tested in version 2.30.2)
- stats (tested in version 3.4.3)
- utils (tested in version 3.4.3)
- usethis (tested in version 1.3.0)
Pre-requisite packages viz. stats, utils and usethis can be installed from CRAN whereas ChemmineR can be installed from bioconductor using the following commands:
## stats Installation
install.packages("stats")## utils Installation
install.packages("utils")## usethis Installation
install.packages("usethis")## ChemmineR Installation (For R < Version 3.5)
source("https://bioconductor.org/biocLite.R")
biocLite("ChemmineR")
## ChemmineR Installation (For R >= Version 3.5)
install.packages("BiocManager")
BiocManager::install("ChemmineR", version = "3.8")The package can be installed from CRAN (recommended).
## CMD Installation
install.packages("uCAREChemSuiteCLI")We have provided examplary file under uCAREChemSuiteCLI/inst/extdata/
Run the algorithm using the provided examples with the following command:
# Loading libraries
library("uCAREChemSuiteCLI")# Run drug.class.deterministic
example.class.deterministic<- system.file('extdata/example.sdf', package="uCAREChemSuiteCLI")
drug.class.deterministic(example.class.deterministic)# Run drug.class.stochastic
example.class.stochastic<- system.file('extdata/example.sdf', package="uCAREChemSuiteCLI")
drug.class.stochastic(example.class.stochastic,"3","0.25")# Run drug.resistome.deterministic
example.resistome.deterministic<- system.file('extdata/example.sdf', package="uCAREChemSuiteCLI")
drug.resistome.deterministic(example.resistome.deterministic, "1")# Run drug.resistome.stochastic
example.resistome.stochastic<- system.file('extdata/example.sdf', package="uCAREChemSuiteCLI")
drug.resistome.stochastic(example.resistome.stochastic, "3", "0.25", "1")All functions are well documented. You can find additional information such as input arguments and function abstract using R help function. eg. ??drug.class.deterministic
Please report any issues or bugs you find while installing/running uCAREChemSuiteCLI to:
- Saurav Bhaskar Saha [[email protected]] :)
uCAREChemSuiteCLI is under MIT License.