Convert glycan composition to glycan structure

Given glycan compositions, this function matches them to all possible glycan structures in the glydb database.

Usage

comp_to_struc(comps, db = NULL)

Arguments

comps

Glycan compositions to match against. Can be either:

A glyrepr::glycan_composition() vector.
Byonic style composition strings (e.g. Hex(5)HexNAc(2)).
Simple style composition strings (e.g. H5N4F1S1).

db

Glycan structures to match against. Can be a glyrepr::glycan_structure() vector or any structure strings supported by glyparse::auto_parse(). If not provided, glydb::glydb_structures(structure_level = "intact") will be used.

Value

A tibble with the following columns:

composition: The glycan compositions, as glyrepr::glycan_composition() vector.
structure: The possible glycan structures, as glyrepr::glycan_structure() vector. Note that one glycan composition can have multiple rows in the result, corresponding to different possible glycan structures.

Note about monosaccharide types

See glyrepr::get_mono_type() for the definition of monosaccharide types. This function is designed to work with glycans with both generic and concrete monosaccharides. It follows the rules:

Generic compositions in comps can match both generic and concrete structures in db.
Concrete compositions in comps can only match concrete structures in db.

How to set `db`

The db parameter is very important for all functions in this package. By default, it uses all available glycans in the glydb package, which is usually larger than what you need. You can use helper functions in glydb to narrow down the database, e.g. glydb::glydb_compositions() or glydb::glydb_structures().

You can use the species and glycan_type parameters to focus on specific species and glycan type. For example, if you are only interested in N-glycan compositions in human, you can use glydb::glydb_compositions(species = "Homo sapiens", glycan_type = "N"). Also, you can decide the level of information in the database by setting mono_type of glydb::glydb_compositions() and structure_level of glydb::glydb_structures().

You can then pass the result to the db parameter of this function. For example,

my_db <- glydb::glydb_compositions(species = "Homo sapiens", glycan_type = "N")
mz_to_comp(mz, db = my_db)

Examples

comp_to_struc("H5N2")
#> # A tibble: 77 × 2
#>    composition     structure                                                    
#>    <comp>          <struct>                                                     
#>  1 Hex(5)HexNAc(2) Man(b1-2)Man(b1-3)[Man(b1-3)Man(b1-6)]Man(b1-4)GlcNAc(b1-4)G…
#>  2 Hex(5)HexNAc(2) GlcNAc(b1-2)Man(a1-3)[Man(a1-3)[Man(a1-6)]Man(a1-6)]Man(b1-4…
#>  3 Hex(5)HexNAc(2) Man(a1-2)Man(a1-3)[Man(a1-3)Man(a1-6)]Man(b1-4)GlcNAc(b1-4)G…
#>  4 Hex(5)HexNAc(2) Man(a1-3)[Man(a1-6)]Man(a1-6)[Man(a1-3)]Man(a1-4)GlcNAc(b1-4…
#>  5 Hex(5)HexNAc(2) Man(a1-2)Man(a1-2)Man(a1-3)[Glc(a1-6)]Man(b1-4)GlcNAc(b1-4)G…
#>  6 Hex(5)HexNAc(2) Man(a1-3)Man(a1-3)[Man(a1-3)Man(a1-6)]Man(b1-4)GlcNAc(b1-4)G…
#>  7 Hex(5)HexNAc(2) Man(a1-3)[Man(a1-6)]Man(a1-6)Man(a1-3)Man(b1-4)GlcNAc(b1-4)G…
#>  8 Hex(5)HexNAc(2) Man(a1-2)Man(a1-3)[Man(a1-6)Man(a1-6)]Man(a1-4)GlcNAc(b1-4)G…
#>  9 Hex(5)HexNAc(2) Man(a1-2)Man(a1-3)Man(a1-6)[Man(a1-3)]Man(b1-4)GlcNAc(b1-4)G…
#> 10 Hex(5)HexNAc(2) Gal(a1-6)Man(b1-3)[Man(b1-6)Man(a1-6)]Man(b1-4)GlcNAc(b1-4)G…
#> # ℹ 67 more rows