Changelog

glyclean 0.14.1

Minor improvements and bug fixes

• auto_clean() is now out-of-box without needing to install other packages (#15).
• Reimplement impute_min_prob() to avoid the dependency on imputeLCMD package (#16).

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).

glyclean 0.13.0

New features

• transform_clr() and transform_alr() now align with the methods described in DOI: 10.1038/s41467-025-56249-3.
• auto_normalize() now only performs total abundance normalization for glycomics data.
• Add auto_coda() to use the CoDA strategy in glycowork for glycomics data.

glyclean 0.12.2

New features

• Add transform_clr() for Centered Log-Ratio (CLR) transformation.
• Add transform_alr() for Additive Log-Ratio (ALR) transformation.

Minor improvements and bug fixes

• Update documentation of auto_clean() for QC-related behaviors.

glyclean 0.12.1

Minor improvements and bug fixes

• Update dependency strategy to use the r-universe repository.

glyclean 0.12.0

New features

• Add method parameter to correct_batch_effect() supporting limma method for batch correction.

Minor improvements and bug fixes

• Fix method handling in correct_batch_effect() for glyexp_experiment method.
• Fix long example line to avoid Rd line width note.

glyclean 0.11.0

New features

• Added automatic UniProt sequence fetching when FASTA is NULL in add_site_seq().
• aggregate() now calls glyexp::standardize_variable() after aggregation to ensure meaningful variable names.

glyclean 0.10.1

Minor improvements and fixes

• Fix a bug that the qc_name argument and group_col argument were ignored in auto_clean().
• The qc_name argument in auto_xxx() functions now can be NULL.

glyclean 0.10.0

New features

• Added a comprehensive suite of Quality Control (QC) plotting functions:
  • plot_missing_heatmap(): Binary heatmap of missing value patterns.
  • plot_missing_bar(): Bar plot of missing proportions by sample or variable.
  • plot_tic_bar(): Total intensity (TIC) bar plot by sample.
  • plot_rank_abundance(): Protein rank abundance plot.
  • plot_int_boxplot(): Log2-intensity boxplots by sample, with optional grouping.
  • plot_rle(): Relative Log Expression (RLE) boxplots for detecting sample-wise bias.
  • plot_cv_dent(): CV density plot, with optional stratified groups.
  • plot_batch_pca(): PCA score plot colored by batch.
  • plot_rep_scatter(): Scatter plots of replicate sample pairs with $R^2$ values.

Minor improvements and fixes

• Add pheatmap, ggplotify, factoextra, and patchwork to Suggests to support enhanced QC visualizations.
• Document and provide examples for the new QC functions in the main vignette.

glyclean 0.9.1

Minor improvements and fixes

• Optimize the message printing of auto_xxx() functions.

glyclean 0.9.0

Breaking changes

• auto_clean() has been redesigned to be more flexible and robust. It now calls auto_normalize(), auto_remove(), auto_impute(), auto_aggregate(), and auto_correct_batch_effect() in sequence, depending on the experiment type.

New features

• Add auto_normalize() to automatically normalize the data.
• Add auto_remove() to automatically remove variables with too many missing values.
• Add auto_impute() to automatically impute the missing values.
• Add auto_aggregate() to automatically aggregate the data.
• Add auto_correct_batch_effect() to automatically correct the batch effects.

Minor improvements and fixes

• remove_xxx() functions now print a message about the number and proportion of variables removed.
• Add a seed argument to impute_miss_forest() to make the imputation results reproducible.
• normalize_median() now issues a warning if any sample has a median value of 0, producing all NaNs in the result.
• correct_batch_effect() now uses a new method to detect group-batch confounding. It uses Cramer’s V to measure the strength of the association between batch and group variables.
• Fix an error in correct_batch_effect() examples.

glyclean 0.8.1

Minor improvements and fixes

• glyclean now depends on the CRAN version of glyrepr.

glyclean 0.8.0

Breaking changes

• Rename remove_missing_variables() to remove_rare().

New features

• All functions in glyclean are generic now. This makes it easier to extend glyclean to other data types.
• Add remove_low_var() for removing variables with low variance.
• Add remove_low_cv() for removing variables with low coefficient of variation.
• Add remove_constant() for removing constant variables.
• Add remove_low_expr() for removing variables with low expression or abundance.

Minor improvements

• Update documentation to include the newly added functions.

glyclean 0.7.1

Minor improvements and bug fixes

• Fix bugs introduced by the breaking changes in glyexp 0.10.0.

glyclean 0.7.0

Breaking changes

• aggregate() now has a new logic for aggregating glycoproteomics data. Instead of dropping all other columns, aggregate() now keeps columns intelligently. Common columns including “gene” will be kept in this way. This new logic has an important implication: columns added by functions like glymotif::add_motif_lgl() or glydet::add_meta_properties() will be kept.

Minor improvements and bug fixes

• Better error message for aggregate() when the user tries to aggregate to a level demanding structure but the structure column is missing.
• Explicitly check if sva package is installed in correct_batch_effect().
• Update dependencies to explicitly require tibble and glyexp.

glyclean 0.6.4

Minor improvements and bug fixes

• Update dependencies to depend on release versions of glycoverse packages.

glyclean 0.6.3

Bug fixes

• Fix bugs in documentation examples due to breaking changes introduced in glyexp 0.8.0.

glyclean 0.6.2

Bug fixes

• Add scales to Imports.

glyclean 0.6.1

Minor improvements

• Update the documentation of aggregate().

Bug fixes

• Fix a bug in aggregate() where it falled on experiments returned by most glyread functions.

glyclean 0.6.0

Major changes

• Add add_site_seq() function to add site sequences to a glycopeptide experiment.

glyclean 0.5.0

Major changes

• Add infer_protein() function to resolve multiple protein assignments for glycopeptides.
• Add adjust_protein() function to remove protein expression from glycopeptide expression.

Minor improvements

• Rename the first argument of aggregate() from x to exp to be consistent with other functions.

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().