methylcheck.run_qc

methylcheck.run_qc(path)

Generates all QC plots for a dataset in the path provided. if process –all was used to create control probes and raw values for QC, because it uses four output files:

• beta_values.pkl
• control_probes.pkl
• meth_values.pkl or noob_meth_values.pkl
• unmeth_values.pkl or noob_unmeth_values.pkl

output is all to screen, so best to use in a jupyter notebook. If you prefer output in a PDF, use ReportPDF instead.

Note: this will only look in the path folder; it doesn’t do a recursive search for matching files.