Step: Infer Glycan Structures

Infer glycan structures from the glycan_composition column in var_info. This step uses glyanno::comp_to_struc() with a structure database from glydb::glydb_structures() and keeps only variables with an inferred structure.

This step requires exp (experiment data).

Usage

step_infer_structure(species = NULL, structure_level = "topological")

Arguments

species: Species name used to restrict the glycan structure database. Default is NULL, which does not restrict by species.
structure_level: Structure level passed to glydb::glydb_structures(). One of "intact", "topological", or "basic". Default is "topological".

Value

A glysmith_step object.

Details

Data required:

exp: The experiment whose glycan structures should be inferred

Data generated:

uninferred_exp: The original experiment before structure inference

Tables generated:

inferred_structures: A table containing the inferred structure for each original variable and whether inference succeeded.

AI Prompt

This section is for AI in inquire_blueprint() only.

Include this step when the user requests structure-aware analysis but the experiment has glycan compositions and no glycan structures.
This step should be placed before step_derive_traits(), step_quantify_dynamic_motifs(), or step_quantify_branch_motifs().
Mention that variables without inferred structures are removed.
Always ask for species restriction to improve inference accuracy, but allow users to skip it if they want.

Examples

step_infer_structure()
#> <step "step_infer_structure()"> Glycan structure inference
step_infer_structure(species = "Homo sapiens")
#> <step "step_infer_structure(species = \"Homo sapiens\")"> Glycan structure
#> inference