Changelog

glydet 0.5.0

The meta-property T is renamed to Tp, to avoid confusion with the R alias T for TRUE.

Add mp_cols parameter to derive_traits() as a new way to define custom meta-properties.

derive_traits() and derive_traits_() now have separate documentations.
Update the “Defining Custom Traits” vignette to include the newly added mp_cols parameter.
Better error message when custom derived traits use undefined meta-properties.
Add a section about how NAs can appear in the documentations of prop(), ratio(), and wmean().

The old all_traits() is renamed to basic_traits().
A new all_traits() is added, which includes more advanced derived traits with more detailed within conditions.
derive_traits() now uses basic_traits() by default.
derive_traits() now returns a glyexp::experiment() object with the “traitomics” type for glycomics data, and “traitproteomics” type for glycoproteomics data, instead of “traitomics” for all input.

Add missForest to the Suggests field in DESCRIPTION. This package is used in vignettes to impute missing values for glycomics data.

Trait functions created by prop(), ratio(), and wmean() can be printed nicely into the console.
Add explain_trait() to provide a human-readable explanation of trait definitions.
Add a nF built-in meta-property to count the number of fucoses. The TF trait is redefined as prop(nF > 0).

Emphasize in the documentation of derive_traits() and derive_traits_() that the “glycan_structure” column can be either a glyrepr::glycan_structure() vector or a character vector of glycan structure strings supported by glyparse::auto_parse().
derive_traits() and derive_traits_() now raise an error if the trait_fns parameter is not a named list.
derive_traits() and derive_traits_() now raise an error if the trait_fns parameter is an empty list.
A “Working with Glycomics Data” section is added to the “Get Started” vignette.
A “Validating Trait Definitions” section is added to the “Defining Custom Traits” vignette.

derive_traits() and add_meta_properties() now validates if the struc_col column exists.
Add an overwrite parameter to add_meta_properties() to deal with existing trait columns.

Fix a serious bug in derive_traits(), where the row names of the expression matrix were not set correctly for glycomics data.
Fix typos in documentations.