methylcheck is a Python-based package for filtering and visualizing Illumina methylation array data. The focus is on quality control.
Methylcheck is designed to accept the output from the Methylprep package. It 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.
This package is available in PyPi.
pip install methylcheck
How to use it¶
In general, the best way to import data is to use
methylprep and run
run_pipeline(data_folder, betas=True), collect the beta_values.pkl file it returns/saves to disk, and load that in a Jupyter notebook with methylcheck. From there, each data transformation is a single line of code using Panadas DataFrames.
methylcheck will keep track of the data format/structures for you, and you can visualize the effect of each filter as you go. You can also export images of your charts for publication.
Refer to the Jupyter notebooks on readthedocs for examples of filtering probes from a batch of samples, removing outlier samples, and generating plots of data.