Execution

This section assumes you have already installed the package. If not, please visit the installation section.

Environment Setup

An environment specification is provided in the repository (environment.yaml). We recommend using miniconda to create an environment containing all dependencies needed for this package to run. If you need to install miniconda, you can find instructions here. Once miniconda is configured, create the environment:

conda install mamba
mamba env create -f environment.yaml

Activate the environment and launch an R terminal:

conda activate process.phenotypes
R

Run process.phenotypes

First, load the library in an R instance:

library(process.phenotypes)

The entry point for the software is process.phenotypes::create.phenotype.report. You can get useful help documentation for this function in the usual R manner: ?process.phenotypes::create.phenotype.report. An example run command might be:

process.phenotypes::create.phenotype.report("/path/to/input-phenotypes.tsv",
                                            "yaml-configuration/dataset-specific.yaml",
                                            "yaml-configuration/shared-models.yaml",
                                            "/path/to/output.html")