Changelog

glyexp 0.10.1

Minor improvements and fixes

• glyexp now depends on the CRAN version of glyrepr.

glyexp 0.10.0

This version is a big update for experiment(). We have made this function more flexible, robust, and user-friendly. The breaking changes we introduced in this version have a broad impact on many glycoverse packages. So we recommend to update all packages to the latest versions.

Breaking Changes

• experiment() now checks whether certain columns are present in var_info. For “glycomics” experiments, glycan_composition is required. For “glycoproteomics” experiments, protein, protein_site, and glycan_composition are required. If any required column is missing, an error will be raised.

New Features

• experiment() now intelligently coerce common column types to improve user experience. For example, it will convert character to factor for the “group” column in sample_info. This behavior can be controlled by the coerce_col_types argument.
• experiment() now checks the column types for some important columns, such as protein, protein_site, glycan_composition, etc. The checking is performed after column coercion (if coerce_col_types is TRUE), and only a message is printed if some column type conventions are violated. This behavior can be controlled by the check_col_types argument.
• Add a new type of experiment: “others”. This type is for other omics experiments that are not glycoproteomics or glycomics. In this case, glycan_type can be NULL. Also, type coercion and checking are skipped for this type.
• Now the minimum required input for experiment() is only an expression matrix. If not provided, sample_info and var_info will be automatically generated based on the column and row names of the expression matrix. exp_type will be set to “others” and glycan_type will be set to NULL. This gives users more flexibility to create experiment() objects.
• “traitomics” and “traitproteomics” are valid values for exp_type of experiment() now.

Minor Improvements and Bug Fixes

• toy_experiment now has exp_type “others”.
• real_experiment and real_experiment2 now have factors for the “group” column in sample_info.
• Update the “Creating Experiments” vignette to reflect the new changes.
• set_meta_data(), set_exp_type(), and set_glycan_type() now check the meta data.
• get_meta_data() now returns all meta data fields if x is NULL.

glyexp 0.9.2

Minor improvements and bug fixes

• Printing the experiment() object now includes the experiment type in the title.
• Add a vignette to explain four experiment types.
• Add a vignette of creating an experiment() object from scratch.

glyexp 0.9.1

Minor improvements and bug fixes

• Import := from rlang to fix “could not find function”%||%“” bug in as_se() and from_se() in some systems.

glyexp 0.9.0

New features

• Add real_experiment2, a glycomics example experiment.
• Add from_se() and as_se() to convert experiment() to and from SummarizedExperiment() objects.
• Add split() to split an experiment into a list of experiments.

Minor improvements and bug fixes

• Add merge() and split() to the getting started vignette.
• Add a picture to the getting started vignette to explain index columns.
• Fix a typo in toy_experiment: “N3N2” should be “H3N2”.
• Fix an error in the documentation of select_var().

glyexp 0.8.0

Breaking changes

• toy_experiment is no longer a function, but a data object. Instead of using toy_experiment() to get the example experiment, use toy_experiment directly.

New features

• Add left_join_obs(), left_join_var(), inner_join_obs(), inner_join_var(), semi_join_obs(), semi_join_var(), anti_join_obs(), and anti_join_var(). These functions are useful for adding new information to experiment() from tibbles.
• Add a real_experiment data object. This is derived from a real-world N-glycoproteome dataset.

Minor improvements and bug fixes

• Fix warnings in merge().
• Column types in sample_info and var_info are now displayed in the console when printing the experiment() object.
• set_exp_type() and set_glycan_type() now validate the input values.

glyexp 0.7.0

Major changes

• Add merge() function to merge two experiments.

Minor improvements

• Update the documentation of experiment().

glyexp 0.6.0

Major changes

• Add a series of functions to describe the experiment:
  • count_compositions(): The number of glycan compositions.
  • count_structures(): The number of glycan structures.
  • count_peptides(): The number of peptides.
  • count_glycopeptides(): The number of unique combinations of peptides, sites, and glycans.
  • count_glycoforms(): The number of unique combinations of proteins, sites, and glycans.
  • count_proteins(): The number of proteins.
  • count_glycosites(): The number of unique combinations of proteins and sites.
• Remove add_glycan_descriptions(), add_struc_descriptions(), and add_comp_descriptions(). These functions are moved to the glymotif package.