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Step: Infer Glycan Structures

step_infer_structure.Rd

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.

See also

glyanno::comp_to_struc(), glydb::glydb_structures()

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