Changelog

glyclean 0.4.0

Major changes

• All data processing functions now accept matrices as input in addition to glyexp_experiment objects.
• The by parameter in data processing functions now accepts factors in addition to column names, enabling direct use with matrix inputs.
• API updated to support custom grouping factors for batch operations when working with matrices.

Minor improvements

• Improved error messages for correct_batch_effect() and detect_batch_effect() when column names are not found in sample information.
• More meaningful error messages when providing column names as batch or group arguments with matrix inputs.
• Enhanced parameter validation and error handling across all modules.

Bug fixes

• Fixed incorrect behavior of by argument in filter_missing_variable().
• Resolved issues with parameter processing when using different input types.

glyclean 0.3.0

• auto_clean() now detects batch effects before batch correction.
• to_level argument is removed from auto_clean().