Enhance glycan structure

Given a glycan structure of any resolution level (see glyrepr::get_structure_level() for details), this function gives all possible glycan structures of higher resolution level.

Usage

enhance_struc(strucs, to_level = "intact", db = NULL)

Arguments

strucs

A glyrepr::glycan_structure() vector, or a character vector of glycan structure strings supported by glyparse::auto_parse(). Glycan structures with level higher or same as to_level will be returned as is. Glycan structures with level lower than to_level will be enhanced to the level of to_level.

to_level

The resolution level to enhance to. Can be "intact" or "topological". Default is "intact".

db

A glydb::glydb_structures() vector, or a character vector of glycan structure strings supported by glyparse::auto_parse(). All structures in db must be at the same resolution level as to_level. If not provided, a default structure vector is loaded from glydb::glydb_structures() with the specified to_level.

Value

A tibble with the following columns:

• raw: The original glycan structures.

• enhanced: The enhanced glycan structures. Note that one raw glycan structure can have different enhanced glycan structures as multiple rows in the result.

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

# From topological level to intact level
enhance_struc("Gal(??-?)GalNAc(??-", to_level = "intact")
#> # A tibble: 9 × 2
#>   raw                 enhanced           
#>   <struct>            <struct>           
#> 1 Gal(??-?)GalNAc(??- Gal(b1-3)GalNAc(a1-
#> 2 Gal(??-?)GalNAc(??- Gal(b1-3)GalNAc(b1-
#> 3 Gal(??-?)GalNAc(??- Gal(a1-3)GalNAc(b1-
#> 4 Gal(??-?)GalNAc(??- Gal(b1-4)GalNAc(b1-
#> 5 Gal(??-?)GalNAc(??- Gal(a1-6)GalNAc(a1-
#> 6 Gal(??-?)GalNAc(??- Gal(b1-6)GalNAc(a1-
#> 7 Gal(??-?)GalNAc(??- Gal(b1-6)GalNAc(b1-
#> 8 Gal(??-?)GalNAc(??- Gal(a1-3)GalNAc(a1-
#> 9 Gal(??-?)GalNAc(??- Gal(b1-4)GalNAc(a1-

# From basic level to topological level
enhance_struc("Hex(??-?)HexNAc(??-", to_level = "topological")
#> # A tibble: 4 × 2
#>   raw                 enhanced           
#>   <struct>            <struct>           
#> 1 Hex(??-?)HexNAc(??- Gal(??-?)GalNAc(??-
#> 2 Hex(??-?)HexNAc(??- Gal(??-?)GlcNAc(??-
#> 3 Hex(??-?)HexNAc(??- Glc(??-?)GlcNAc(??-
#> 4 Hex(??-?)HexNAc(??- Man(??-?)GlcNAc(??-

# From partial level to intact level
enhance_struc("Gal(b1-?)GalNAc(a1-", to_level = "intact")
#> # A tibble: 3 × 2
#>   raw                 enhanced           
#>   <struct>            <struct>           
#> 1 Gal(b1-?)GalNAc(a1- Gal(b1-3)GalNAc(a1-
#> 2 Gal(b1-?)GalNAc(a1- Gal(b1-6)GalNAc(a1-
#> 3 Gal(b1-?)GalNAc(a1- Gal(b1-4)GalNAc(a1-