methylprep Package

The methylprep package contains both high-level APIs for processing data from local files and low-level functionality allowing you to customize the flow of data and how it is processed.


High-Level Processing

The primary methylprep API provides methods for the most common data processing and file retrieval functionality.

run_pipeline

Run the complete methylation processing pipeline for the given project directory, optionally exporting the results to file.

Returns: A collection of DataContainer objects for each processed sample

from methylprep import run_pipeline

data_containers = run_pipeline(data_dir, array_type=None, export=False, manifest_filepath=None, sample_sheet_filepath=None, sample_names=None)
Argument Type Default Description
data_dir str, Path
Base directory of the sample sheet and associated IDAT files
array_type str None Code of the array type being processed. Possible values are custom, 450k, epic, and epic+. If not provided, the pacakage will attempt to determine the array type based on the number of probes in the raw data.
export bool False Whether to export the processed data to CSV
manifest_filepath str, Path None File path for the array’s manifest file. If not provided, this file will be downloaded from a Life Epigenetics archive.
sample_sheet_filepath str, Path None File path of the project’s sample sheet. If not provided, the package will try to find one based on the supplied data directory path.
sample_names str collection None List of sample names to process. If provided, only those samples specified will be processed. Otherwise all samples found in the sample sheet will be processed.

get_sample_sheet

Find and parse the sample sheet for the provided project directory path.

Returns: A SampleSheet object containing the parsed sample information from the project’s sample sheet file

from methylprep import get_sample_sheet

sample_sheet = get_sample_sheet(dir_path, filepath=None)
Argument Type Default Description
data_dir str, Path
Base directory of the sample sheet and associated IDAT files
sample_sheet_filepath str, Path None File path of the project’s sample sheet. If not provided, the package will try to find one based on the supplied data directory path.

get_manifest

Find and parse the manifest file for the processed array type.

Returns: A Manifest object containing the parsed probe information for the processed array type

from methylprep import get_manifest

manifest = get_manifest(raw_datasets, array_type=None, manifest_filepath=None)
Argument Type Default Description
raw_datasets RawDataset collection
Collection of RawDataset objects containing probe information from the raw IDAT files.
array_type str None Code of the array type being processed. Possible values are custom, 450k, epic, and epic+. If not provided, the pacakage will attempt to determine the array type based on the provided RawDataset objects.
manifest_filepath str, Path None File path for the array’s manifest file. If not provided, this file will be downloaded from a Life Epigenetics archive.

get_raw_datasets

Find and parse the IDAT files for samples within a project’s sample sheet.

Returns: A collection of RawDataset objects for each sample’s IDAT file pair.

from methylprep import get_raw_datasets

raw_datasets = get_raw_datasets(sample_sheet, sample_names=None)
Argument Type Default Description
sample_sheet SampleSheet
A SampleSheet instance from a valid project sample sheet file.
sample_names str collection None List of sample names to process. If provided, only those samples specified will be processed. Otherwise all samples found in the sample sheet will be processed.

Low-Level Processing