LINDA+

This repository contains the scripts for the ILP (Integer Linear Programming) implementation of the LINDA+ R package and accompanying scripts that implement the method. ILP is a mathematical optimisation algorithm in which the objective function and constraints are linear and the variables are integers. The dedicated documentation page of LINDA+ which describes the inputs and the outputs as well as tutorials has been provided here.

License

Distributed under the GNU GPLv3 License.

Installation

1. Solver Prerequisites

Before installing LINDA+, please keep in mind the following solver pre-requisites:

LINDA+ requires the interactive version of IBM Cplex as an ILP problem optimiser. The IBM ILOG Cplex is freely available through Academic Initiative.

Details about how to obtain the free full license under the Academic Initiative have been provided here.

Once the CPLEX solver has been acquired by the user, they must save the executable files in any desired location in the machine they are using and then they can run. Then, thy should make the acquired cplex solver executable, but running the following (in MAC/Unix systems): chmod +x cplex. Finally, you can perform the LINDA+ analyses after specifying the path to the executable file (through the solverPath parameter, see examples below).

2. Package Depedencies

Additionally before installation, the users must install the following R-package depedencies: igraph, aggregation and xml2.

3. Package installation

Once the required solvers have been obtained and the mentioned R-package depedencies have been installed, then the users can proceed with the installation of LINDA.

Currently users can install LINDA directly from the source after downloading the source (tar file) and typing in R command line the following:

# directly from GitHub
devtools::install_github("dieterich-lab/LINDAPlus", build_vignettes = FALSE)

# or download the source file from GitHub and install from source
devtools::install_local(path = "path_to_extracted_LINDAPlus_directory", build_manual = TRUE, build_vignettes = FALSE, force = TRUE)

NOTE: If you wish for the the Vignettes to be built and for the test example to run successfully, please put the cplex executable file under the /Downloads/ directory and only then you can set build_vignettes = TRUE. In the case when building the vignettes is not possible, you can access it here.

Upon installation of the package, you can check on the package Vignettes:

# check vignettes
vignette("LINDAPlus")

# check documentation of the main function
?runLINDAPlus

Running LINDA+

The LINDA library can be initialized by:

library(LINDAPlus)

A documentation of the current version of the main runLINDAPlus() function can be obtained by simply typing ?runLINDAPlus in R once the package has been installed.

Examples

Examples have been provided on the vignettes of the package which can be accessed here or by typing vignette("LINDAPlus") in the R console.

This package is an ongoing work and it is currently being updated