Installation R

Installation - R (R-wrapper)

This section will help you set up the necessary software and packages required to run SigProfilerMatrixGeneratorR.

Important: You must first install the Python package for SigProfilerMatrixGenerator before installing the R wrapper.

Prerequisites

• Internet Connection
• Python - v3.4+
• pandas - any version (automatically downloaded with SigProfilerMatrixGenerator)
• Wget - v1.9
• SigProfilerPlotting - latest version (automatically downloaded with SigProfilerMatrixGenerator)
• Reference genomes - At least one reference genome must be downloaded and installed prior to use

Step 1: Install Python Package

First, follow the Python Installation instructions to install the base SigProfilerMatrixGenerator package:

pip install SigProfilerMatrixGenerator

Step 2: Install R Dependencies

You must first install the devtools and reticulate libraries in R:

R
> install.packages("devtools")
> install.packages("reticulate")

Step 3: Install SigProfilerMatrixGeneratorR

Once the dependencies are installed, you can install SigProfilerMatrixGeneratorR:

R
> library("reticulate")
> use_python("path_to_your_python3")
> py_config()
> library("devtools")
> install_github("SigProfilerSuite/SigProfilerMatrixGeneratorR")

Replace "path_to_your_python3" with the actual path to your Python 3 installation (e.g., /usr/local/bin/python3 or the path from your conda environment).

Step 4: Install Reference Genome

Prior to use of SigProfilerMatrixGeneratorR, the reference genome files need to be installed:

R
> library("SigProfilerMatrixGeneratorR")
> install('GRCh37', rsync=FALSE, bash=TRUE)

This example installs the human GRCh37 assembly reference files. You can install any of the available genome assemblies.

Note: The installation process saves custom reference files for all chromosomes in the genome assembly, requiring ~3 GB of storage per genome.

Setting up R Environment with Conda (Recommended)

For a streamlined setup, you can use conda to create an environment with all dependencies:

conda create --name spmg_r -y
conda activate spmg_r
conda install python=3.10 r-base r-devtools r-reticulate -c conda-forge -y
pip install SigProfilerMatrixGenerator
echo 'devtools::install_github("SigProfilerSuite/SigProfilerMatrixGeneratorR")' | Rscript -

Upgrades

To upgrade SigProfilerMatrixGenerator:

pip install SigProfilerMatrixGenerator --upgrade

Then reinstall the R package:

R
> library("devtools")
> install_github("SigProfilerSuite/SigProfilerMatrixGeneratorR")