Changelog

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.