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Enhance glycan composition

enhance_comp.Rd

Given a generic glycan composition (e.g. Hex(5)HexNAc(2)), this function gives all possible concrete glycan compositions (e.g. Man(5)GlcNAc(2)).

Usage

enhance_comp(comps, db = NULL)

Arguments

comps

A glyrepr::glycan_composition() vector, or a character vector of glycan composition strings of Byonic or simple style (e.g. "Hex(5)HexNAc(2)", "H5N4F1S1"). Generic compositions (e.g. Hex(5)HexNAc(2)) will be matched to all possible concrete compositions in db. Concrete compositions (e.g. Man(5)GlcNAc(2)) will be returned as is.

db

A glydb::glydb_compositions() vector, or a character vector of glycan composition strings of Byonic or simple style (e.g. "Man(5)GlcNAc(2)", "H5N4F1S1"). All compositions in db must be concrete (e.g. Man(5)GlcNAc(2)). If not provided, glydb::glydb_compositions(mono_type = "concrete") will be used.

Value

A tibble with the following columns:

  • raw: The original compositions.

  • enhanced: The enhanced compositions. Note that one raw composition can have different enhanced compositions 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

enhance_comp("Hex(5)HexNAc(2)")
#> # A tibble: 5 × 2
#>   raw             enhanced             
#>   <comp>          <comp>               
#> 1 Hex(5)HexNAc(2) Man(5)GlcNAc(2)      
#> 2 Hex(5)HexNAc(2) Glc(1)Man(4)GlcNAc(2)
#> 3 Hex(5)HexNAc(2) Man(4)Gal(1)GlcNAc(2)
#> 4 Hex(5)HexNAc(2) Glc(1)Gal(4)GlcNAc(2)
#> 5 Hex(5)HexNAc(2) Man(3)Gal(2)GlcNAc(2)