Changelog

Source: NEWS.md

glyexp (development version)

glyexp 0.12.4

Minor improvements and bug fixes

• Update real_experiment and real_experiment2 to use new implementation of glyrepr_structure and glyrepr_composition in the development version of glyrepr.

glyexp 0.12.3

Minor improvements and bug fixes

• Fix standardize_variable() failing for many proteins due to UniProt API URL length limits. Queries are now batched to stay within limits.

glyexp 0.12.2

Minor improvements and bug fixes

• Fix UniProt.ws API usage to use the correct endpoint for mapping UniProt IDs to gene symbols.

glyexp 0.12.1

New features

• standardize_variable() now uses “X” for site when protein_site or peptide_site is NA.

glyexp 0.12.0

New features

• Add standardize_variable() to standardize the variable names of an experiment. This function makes variable names more human-readable and meaningful.

Minor improvements and bug fixes

• real_experiment and real_experiment2 now have standardized variable names.
• Fix a problem in real_experiment that the peptide column contains “J” instead of “N” for glycosites.

glyexp 0.11.2

Minor improvements and bug fixes

• filter_obs() and filter_var() now drop unused levels for columns used for filtering. For example, filter_obs(exp, group %in% c("A", "B")) will drop all other levels from the group column in sample_info, keeping only “A” and “B”. This behavior makes downstream analysis easier.
• Fix a logic error in experiment type coercion. Previously, type coercion is performed as long as check_col_types = TRUE, even if coerce_col_types = FALSE. Now, type coercion is performed as long as coerce_col_types = TRUE.
• Update message of experiment() for type coercion and checking.
• Optimize the performance of merge().
• Join functions now don’t throw an error when no samples or variables are left after joining. Instead, they return an empty experiment. This change is to align with the behavior of dplyr::join(), which also returns an empty tibble when no rows are left after joining.
• Update documentation of select_obs() and select_var() to explain that the sample or variable column will always be kept.

glyexp 0.11.1

Breaking changes

• filter_obs() and filter_var() no longer throw an error when no samples or variables are left after filtering. Instead, they return an empty experiment. This change is to align with the behavior of dplyr::filter(), which also returns an empty tibble when no rows are left after filtering.

glyexp 0.11.0

Breaking changes

• Remove count_xxx() functions, as their functionality is now covered by summarize_experiment().
• summarize_experiment() now count both total and per-sample numbers. For example, both the number of compositions identified in total (total_composition) and the average number of compositions detected per sample (composition_per_sample) are in the returned tibble.

glyexp 0.10.4

Minor improvements and bug fixes

• Fix a bug in summarize_experiment() that it fails when required columns are missing.

glyexp 0.10.3

New features

• Add summarize_experiment() to summarize an experiment.

Minor improvements and bug fixes

• Fix input type checking in some functions.

glyexp 0.10.2

Minor improvements and fixes

• glycan_type argument of experiment() and set_glycan_type() now accepts more values, including “N”, “O-GalNAc”, “O-GlcNAc”, “O-Man”, “O-Fuc”, “O-Glc”, and NULL.

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.