Data

Please note that most functions are helper functions and are not meant to be used directly.

pyaging.data._data

pyaging.data._data.download_example_data(data_type, dir='pyaging_data', verbose=True)

Downloads example datasets for various types of biological data used in aging studies.

This function facilitates the download of example datasets for different types of biological data, including methylation, histone mark, RNA-seq, and ATAC-seq data. It is designed to provide quick access to standard datasets for users to test and explore the functionalities of the pyaging package.

Parameters:

data_type str

The type of data to download. Valid options are ‘GSE139307’, ‘GSE130735’, ‘GSE223748’, ‘ENCFF386QWG’, ‘GSE65765’, ‘GSE193140’, and ‘blood_chemistry_example’.

dir str (default: 'pyaging_data')

Retained for backward compatibility. Hugging Face files use its standard cache.

verbose bool (default: True)

Whether to log the output to console with the logger. Defaults to True.

Raises:

ValueError – If the specified data_type is not implemented, a ValueError is raised with a message suggesting the user to request its implementation.

Notes

Return type:

None

The function maps the specified data_type to its corresponding filename in the public pyaging Hugging Face data repository. The datasets represent typical data formats and structures used in aging research.

Examples

>>> download_example_data("methylation")
>>> # This will download the example methylation dataset to the local system.