glyclean 0.14.0

We have made significant updates to auto_clean(). QC-related behaviors are now removed from auto_impute(), auto_normalize(), and auto_remove(), because we realized that depending on CVs in QC samples to determine the imputation or normalization strategy is not robust.

Breaking changes

• The info parameter in auto_xxx() functions is removed. This should not be a problem because this parameter was only used internally (#13).

New features

• auto_impute() now uses a different strategy. When sample size < 30, use impute_min_prob(). When 30 <= sample size < 100, use impute_bpca() for glycomics data and impute_min_prob() for glycoproteomics data. When sample size >= 100, use impute_miss_forest() for glycomics data and impute_bpca() for glycoproteomics data (#8).
• auto_impute() and auto_normalize() do not rely on QC samples to determine the strategy (#8, #9).
• auto_remove() does not take into account the QC samples anymore (a1cb616).

Minor improvements and bug fixes

• qc_name argument in auto_clean(), auto_impute(), auto_normalize(), and auto_remove() is deprecated (#8, #9, #10).
• to_try argument in auto_impute() and auto_normalize() is deprecated. impute_to_try and normalize_to_try arguments in auto_clean() are also deprecated (#8, #9).
• auto_impute() and auto_normalize() now support fallbacks for experiments with "others" type (#8, #9).
• Fix the bug that batch_col argument in auto_clean() is ignored (#12).
• Optimize message printing in auto_xxx() functions (#14).