Get Compositions From Glydb Data — glydb

Get unique glycan compositions from glydb_data as a glyrepr::glycan_composition() vector.

Usage

glydb_compositions(mono_type = "concrete", species = NULL, glycan_type = NULL)

Arguments

mono_type: Either "generic" or "concrete". Default is "concrete". See glyrepr::get_mono_type() for details.
species: A string of specie names. See glydb_species() for available specie names. Default is NULL, which means glycans from all species are included.
glycan_type: A string of glycan types. Can be "N", "O-GalNAc", "O-GlcNAc", "O-Man", "O-Fuc", "O-Glc". Default is NULL, which means glycans of all types are included.

Value

A glyrepr::glycan_composition() vector.

Examples

glydb_compositions()
#> <glycan_composition[1183]>
#> [1] Glc(3)
#> [2] Glc(4)
#> [3] Man(3)GlcNAc(1)
#> [4] Gal(1)GlcNAc(1)GalNAc(2)Fuc(1)Neu5Gc(1)
#> [5] Gal(1)GalNAc(1)
#> [6] Gal(1)GlcNAc(1)GalNAc(1)
#> [7] GlcNAc(1)GalNAc(1)
#> [8] GlcNAc(2)GalNAc(1)
#> [9] GalNAc(2)
#> [10] Gal(1)GlcNAc(1)Fuc(2)
#> ... (1173 more not shown)
glydb_compositions(mono_type = "generic")
#> <glycan_composition[756]>
#> [1] Hex(3)
#> [2] Hex(4)
#> [3] Hex(3)HexNAc(1)
#> [4] Hex(1)HexNAc(3)dHex(1)NeuGc(1)
#> [5] Hex(1)HexNAc(1)
#> [6] Hex(1)HexNAc(2)
#> [7] HexNAc(2)
#> [8] HexNAc(3)
#> [9] Hex(1)HexNAc(1)dHex(2)
#> [10] Hex(3)HexNAc(1)dHex(1)
#> ... (746 more not shown)
glydb_compositions(species = "Homo sapiens")
#> <glycan_composition[578]>
#> [1] Glc(4)
#> [2] Gal(1)GalNAc(1)
#> [3] Gal(1)GlcNAc(1)GalNAc(1)
#> [4] GlcNAc(1)GalNAc(1)
#> [5] GlcNAc(2)GalNAc(1)
#> [6] GalNAc(2)
#> [7] Gal(1)GlcNAc(1)Fuc(2)
#> [8] Glc(1)Gal(2)GlcNAc(1)
#> [9] Glc(1)Gal(2)GlcNAc(1)Fuc(1)
#> [10] Gal(1)GlcNAc(1)Fuc(1)
#> ... (568 more not shown)
glydb_compositions(glycan_type = "N")
#> <glycan_composition[515]>
#> [1] Man(3)GlcNAc(6)Fuc(1)
#> [2] Man(2)Gal(1)GlcNAc(3)Fuc(2)
#> [3] Man(3)Gal(2)GlcNAc(4)Neu5Ac(3)
#> [4] Man(6)GlcNAc(2)
#> [5] Man(3)Gal(3)GlcNAc(5)Fuc(1)Neu5Gc(1)
#> [6] Man(2)GlcNAc(2)Fuc(1)
#> [7] Man(3)Gal(3)GlcNAc(5)Neu5Ac(2)
#> [8] Man(2)GlcNAc(3)
#> [9] Man(3)GlcNAc(7)Fuc(1)
#> [10] Man(3)Gal(2)GlcNAc(4)Fuc(1)Neu5Ac(1)
#> ... (505 more not shown)