Skip to contents

Changelog

glyclean 0.8.0

Breaking changes

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

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