Changelog

glydet 0.9.0

New features

• quantify_motifs() now includes a motif_structure column in the var_info tibble of the returned experiment, containing the parsed glycan structure for each motif.

glydet 0.8.1

Minor improvements and bug fixes

• Fix bugs in explain_trait() and make_trait() that “nGt” was not intepretaed correctly.

glydet 0.8.0

New features

• make_trait() and explain_trait() now have a custom_mp argument to allow users to define custom meta-properties.

Minor improvements and bug fixes

• Update documentation of quantify_motifs() to add a new type of alignment: “exact”, to be consistent with glymotif 0.12.0.
• Add reflection mechanism to make_trait() to make it more accurate.
• Add a verbose argument to make_trait() to control the amount of information printed to the console.

glydet 0.7.0

We introduce exciting new features to glydet, including explaining and creating derived traits using a Large Language Model (LLM). We hope these features will help you work with custom derived traits more efficiently with less effort.

New features

• explain_trait() now supports total() and wsum() traits.
• explain_trait() now supports a new argument use_ai to use a Large Language Model (LLM) to explain the trait.
• Add make_trait() to create a derived trait function using natural language with a Large Language Model (LLM).

Minor improvements and bug fixes

• The result of derive_traits() and derive_traits_() now have an explanation column in the output tibble, explaining the derived traits.

glydet 0.6.5

Minor improvements and fixes

• glydet now depends on the CRAN version of glyparse.

glydet 0.6.4

Minor improvements and fixes

• glydet now depends on the CRAN version of glyrepr.

glydet 0.6.3

Minor improvements and bug fixes

• Updated dependency on glymotif (>= 0.10.0) to ensure compatibility with recent changes in package igraph v2.2.0.

glydet 0.6.2

Minor improvements and bug fixes

• Add alignments and ignore_linkages parameters to quantify_motifs(). These two parameters were left behind when we migrated quantify_motifs() from glymotif to glydet in glydet 0.6.0.

glydet 0.6.1

Minor improvements and bug fixes

• Fix bugs introduced by the breaking changes in glyexp 0.10.0.

glydet 0.6.0

Breaking changes

• The first parameter of wmean() is renamed from val_cond to val.
• The built-in trait SG is renamed to GS, and GA to AG, to match the convention that the last element of a trait name should be the focused property.

New features

• Add two new trait factories: total() and wsum().
• Add quantify_motifs(). This function was once in the glymotif package, but we realized that motif quantification is essentially a special case of derived traits, so we reimplemented it in glydet with a more consistent and powerful interface.

Minor improvements and bug fixes

• Fix some improperly named traits in the “Defining Custom Traits” vignette.
• Fix an error in a code snippet in the “Defining Custom Traits” vignette: prop(nFc + nFa > 0) -> prop((nFc + nFa) > 0).
• Add a vignette about quantifying glycan motifs.
• Update the introduction part in the “Get Started with glydet” vignette.
• All trait factories now have a glydet_trait super class.

glydet 0.5.0

Breaking changes

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

New features

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

Minor improvements and bug fixes

• 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().

glydet 0.4.1

Minor improvements and bug fixes

• Add another example to the “Defining Custom Traits” vignette.
• Use smaller datasets in examples to reduce build time.

glydet 0.4.0

Breaking changes

• 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.

Minor improvements and bug fixes

• Introduce the new all_traits() in the Get Started vignette.
• Add examples to some functions.

glydet 0.3.1

Minor improvements and bug fixes

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

glydet 0.3.0

New features

• 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).

Minor improvements and bug fixes

• 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.

glydet 0.2.0

New features

• 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.

Minor improvements and bug fixes

• 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.

glydet 0.1.1

Minor improvements and bug fixes

• Update dependencies to depend on release versions of glycoverse packages.

glydet 0.1.0

• First release.