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)[source][source]#
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
The directory to deposit the downloaded file. Defaults to “pyaging_data”.
- verbose bool
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 URL and then calls the download function to retrieve the dataset. The datasets are sourced from AWS S3 and are chosen to 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.