moiraine

moiraine is a package for facilitating the construction of a reproducible analysis pipeline for multi-omics data integration. It provides functions to automate data import, pre-processing, transformation, integration through several tools, as well as interpretation and comparison of the integration results. It relies on the targets package to generate reproducible workflows.

Overview

The workflow for a typical multi-omics integration analysis handled with moiraine includes the following steps:

• Data import: this covers the import of omics measurements as well as associated metadata (i.e. information about the omics features and samples) – moiraine relies on the MultiDataSet package to store this information in a consistent format;

• Inspection of the omics datasets: including checking values density distribution, samples overlap between omics datasets, or presence of missing values;

• Preprocessing of the omics datasets: missing values imputation, transformation, and pre-filtering of samples and omics features;

• Integration of the omics datasets by one or more of the supported tools; currently, the following integration methods are covered in moiraine:

  • sPLS and DIABLO from the mixOmics package

  • sO2PLS from the OmicsPLS package

  • MOFA and MEFISTO from the MOFA2 package

• Interpretation of the integration results using standardised visualisations enriched with features and samples metadata;

• Comparison of the integration results obtained by different methods or pre-processing approaches.

An overview of the capabilities of the package is available here.

Installation

You can install the development version of moiraine from GitHub with:

# install.packages("devtools")
devtools::install_github("Plant-Food-Research-Open/moiraine")

Example

To get started, create a new analysis pipeline in your working directory with:

library(moiraine)

create_moiraine_pipeline()

The user manual provides an in-depth walk-through of a multi-omics integration analysis with the package.

Before using moiraine, we encourage you to get familiar with the targets package; the targets manual is a great place to start.