mepylome 0.0.0

Python package for processing Infinum DNA methylation arrays

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mepylome: Methylation Array Analysis Toolkit

Mepylome is a Python toolkit for parsing, processing, and analyzing methylation array IDAT files.

Note: Mepylome is still under construction.

Features

• Support for Illumina array types: 450k, EPIC, EPICv2
• Parsing of IDAT files
• Extraction of methylation signals
• Calculation of copy number variations (CNV) with Plotly plots visualization
• Methylation analysis tool with a graphical browser interface for UMAP analysis and CNV plots
  • Can be run from the command line with minimal setup or customized through a Python script

Installation

From PyPI

You can install mepylome directly from PyPI using pip:

pip install mepylome
pip install mepylome[cgb]

Ensure you install the 'cgb' variant after (!) the regular package (cgb is used for CNV segmentation).

From Source

1. Clone the repository:

git clone https://github.com/brj0/mepylome.git
cd mepylome

2. Build and install the package:

pip install .
pip install .[cgb]

Usage

Parsing and methylation extraction

Refer to tests/basic_usage.py for a detailed example.

Methylation analysis: Command-line interface

Basic usage:

To start the interface, run the following command (you'll need to manually copy directories into the interface):

mepylome

Prefered usage:

For a more streamlined experience, specify the analysis IDAT files directory, reference IDAT directory, and CpG array type. This command also improves UMAP speed by saving betas to disk:

sh

mepylome -a /path/to/idats -r /path/to/ref -c 450k -s

Show All Parameters

To display all available command-line parameters, use:

mepylome --help

C++ parser

Mepylome also includes a C++ parser (_IdatParser) with Python bindings. Due to no significant speed gain, it is currently not included by default. To enable it, install from source after you execute the following command:

export MEPYLOME_CPP=1

Contributing

Contributions are welcome! If you have any bug reports, feature requests, or suggestions, please open an issue or submit a pull request.

License

This project is licensed under the GPL-3.0 license.

Acknowledgements

Mepylome is strongly influenced by [minfi] (https://github.com/hansenlab/minfi) and [conumee2] (https://github.com/hovestadtlab/conumee2). Some functionalities, such as the manifest handler and parser, are adapted from methylprep.