Changelog • glyexp

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.