Manual: uCAREChemSuiteCLI

• Introduction
• Requirements
• Imports
• Installation
• Example
• Usage
• Help
• Bugs
• License

Introduction

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 deterministic model ("drug.class.deterministic") and stochastic model ("drug.class.stochastic") [Unpublished data].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.

Requirements

• R (tested in version 3.4.3)

Imports

• 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)

Installation of Pre-requisite packages

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")

Installation

The package can be installed from CRAN (recommended).

## CMD Installation
 install.packages("uCAREChemSuiteCLI")

Example

We have provided examplary file under uCAREChemSuiteCLI/inst/extdata/

Usage

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")

Help

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

Bugs

Please report any issues or bugs you find while installing/running uCAREChemSuiteCLI to:

• Saurav Bhaskar Saha [saurav.saha@shiats.edu.in] :)

License

uCAREChemSuiteCLI is under MIT License.