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Get Structures From Glydb Data

glydb_structures.Rd

Get unique glycan structures from glydb_data as a glyrepr::glycan_structure() vector.

Usage

glydb_structures(
  structure_level = "intact",
  species = NULL,
  glycan_type = NULL,
  mono_range = NULL,
  mono_type = "concrete"
)

Arguments

structure_level

Either "intact" or "topological". Default is "intact". See glyrepr::get_structure_level() 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 "HMO", "N", "GSL", "GAG", "O", "O-GalNAc", "O-GlcNAc", "O-Man", "O-Fuc", "O-Glc", or "GPI". When "O", all O-linked glycans are included. Specific O-glycan types only include that subtype. Default is NULL, which means glycans of all types are included.

mono_range

A named list for filtering structures by monosaccharide counts. Each element should be an integer vector of length 2 specifying the minimum and maximum count for that monosaccharide. Monosaccharides not specified will be excluded (count = 0). Use NULL for no filtering. See examples for usage.

mono_type

Either "generic" or "concrete". Default is "concrete". See glyrepr::get_mono_type() for details.

Value

A glyrepr::glycan_structure() vector, with a confidence attribute as a numeric vector with the same length.

Confidence

The returned value has a confidence attribute: a numeric vector of the same length as the result containing log-transformed citation counts for each glycan in glydb_data. When multiple glycans are aggregated into lower-resolution structures or compositions, the maximum confidence score is retained.

The confidence attribute is preserved by vector operations that subset, reorder, repeat, combine, or replace glycans. When vectors containing the same glycan with different confidence values are combined, the maximum confidence is used for every occurrence of that glycan.

Examples

glydb_structures()
#> <glydb_structure[8864]>
#> [1] Glc(b1-3)Glc(b1-3)Glc(b1-
#> [2] Glc(b1-4)Glc(b1-4)Glc(b1-4)Glc(b1-
#> [3] Fuc(a1-2)Gal(b1-4)GlcNAc(b1-6)[Fuc(a1-2)Gal(b1-3)]GalNAc(b1-
#> [4] Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-
#> [5] Galf(a1-2)Galf(a1-4)Gal(b1-
#> [6] Fuc(a1-2)[GalNAc(a1-3)]Gal(b1-4)GlcNAc(b1-3)[Neu5Gc(a2-6)]GalNAc(a1-
#> [7] Gal(b1-3)GalNAc(a1-
#> [8] Gal(b1-3)[GlcNAc(b1-6)]GalNAc(a1-
#> [9] GlcNAc(b1-3)GalNAc(a1-
#> [10] GlcNAc(b1-3)[GlcNAc(b1-6)]GalNAc(a1-
#> ... (8854 more not shown)
#> # Unique structures: 8864
glydb_structures(structure_level = "topological")
#> <glydb_structure[8426]>
#> [1] Neu5Gc(??-?)Neu5Gc(??-?)Gal(??-?)Glc(??-
#> [2] Neu5Ac(??-?)Gal(??-?)GlcNAc(??-?)Man(??-?)[Gal(??-?)GlcNAc(??-?)[Gal(??-?)GlcNAc(??-?)]Man(??-?)]Man(??-?)GlcNAc(??-?)GlcNAc(??-
#> [3] Fuc(??-?)Gal(??-?)GlcNAc(??-?)Gal(??-?)GlcNAc(??-
#> [4] GalNAc(??-?)Gal(??-?)Gal(??-?)Glc(??-
#> [5] {Gal(??-?)[Fuc(??-?)]GlcNAc(??-?)|10,11,12,13,14,15}{Gal(??-?)GlcNAc(??-?)|10,11,12,13,14,15}{Neu5Ac(??-?)Gal(??-?)[Fuc(??-?)]GlcNAc(??-?)|10,11,12,13,14,15}Man(??-?)[Man(??-?)]Man(??-?)GlcNAc(??-?)[Fuc(??-?)]GlcNAc(??-
#> [6] Gal(??-?)Gal(??-?)Gal(??-?)Glc(??-
#> [7] GalNAc(??-?)GlcNAc(??-?)Man(??-?)Glc(??-
#> [8] GlcNAc(??-?)Man(??-?)Man(??-?)Glc(??-
#> [9] Gal(??-?)Gal(??-
#> [10] GalNAc4S(??-?)GlcNAc(??-?)Man(??-?)[Man(??-?)]Man(??-?)GlcNAc(??-?)GlcNAc(??-
#> ... (8416 more not shown)
#> # Unique structures: 8426
glydb_structures(mono_type = "generic")
#> <glydb_structure[7916]>
#> [1] Hex(b1-3)Hex(b1-3)Hex(b1-
#> [2] Hex(b1-4)Hex(b1-4)Hex(b1-4)Hex(b1-
#> [3] dHex(a1-2)Hex(b1-4)HexNAc(b1-6)[dHex(a1-2)Hex(b1-3)]HexNAc(b1-
#> [4] Hex(a1-3)[Hex(a1-6)]Hex(b1-4)HexNAc(b1-
#> [5] Hex(a1-2)Hex(a1-4)Hex(b1-
#> [6] dHex(a1-2)[HexNAc(a1-3)]Hex(b1-4)HexNAc(b1-3)[NeuGc(a2-6)]HexNAc(a1-
#> [7] Hex(b1-3)HexNAc(a1-
#> [8] Hex(b1-3)[HexNAc(b1-6)]HexNAc(a1-
#> [9] HexNAc(b1-3)HexNAc(a1-
#> [10] HexNAc(b1-3)[HexNAc(b1-6)]HexNAc(a1-
#> ... (7906 more not shown)
#> # Unique structures: 7916
glydb_structures(structure_level = "topological", mono_type = "generic")
#> <glydb_structure[7841]>
#> [1] NeuGc(??-?)NeuGc(??-?)Hex(??-?)Hex(??-
#> [2] NeuAc(??-?)Hex(??-?)HexNAc(??-?)Hex(??-?)[Hex(??-?)HexNAc(??-?)[Hex(??-?)HexNAc(??-?)]Hex(??-?)]Hex(??-?)HexNAc(??-?)HexNAc(??-
#> [3] dHex(??-?)Hex(??-?)HexNAc(??-?)Hex(??-?)HexNAc(??-
#> [4] HexNAc(??-?)Hex(??-?)Hex(??-?)Hex(??-
#> [5] {Hex(??-?)[dHex(??-?)]HexNAc(??-?)|10,11,12,13,14,15}{Hex(??-?)HexNAc(??-?)|10,11,12,13,14,15}{NeuAc(??-?)Hex(??-?)[dHex(??-?)]HexNAc(??-?)|10,11,12,13,14,15}Hex(??-?)[Hex(??-?)]Hex(??-?)HexNAc(??-?)[dHex(??-?)]HexNAc(??-
#> [6] Hex(??-?)Hex(??-?)Hex(??-?)Hex(??-
#> [7] HexNAc(??-?)HexNAc(??-?)Hex(??-?)Hex(??-
#> [8] Hex(??-?)Hex(??-
#> [9] HexNAc4S(??-?)HexNAc(??-?)Hex(??-?)[Hex(??-?)]Hex(??-?)HexNAc(??-?)HexNAc(??-
#> [10] HexA(??-?)HexNAc(??-?)HexA(??-?)HexNAc(??-
#> ... (7831 more not shown)
#> # Unique structures: 7841
glydb_structures(species = "Homo sapiens")
#> <glydb_structure[1771]>
#> [1] Gal(b1-3)GalNAc(a1-
#> [2] Gal(b1-3)[GlcNAc(b1-6)]GalNAc(a1-
#> [3] GlcNAc(b1-3)GalNAc(a1-
#> [4] GlcNAc(b1-3)[GlcNAc(b1-6)]GalNAc(a1-
#> [5] GalNAc(a1-3)GalNAc(a1-
#> [6] GlcNAc(b1-6)GalNAc(a1-
#> [7] Fuc(a1-2)Gal(b1-3)[Fuc(a1-4)]GlcNAc(b1-
#> [8] Gal(b1-3)GlcNAc(b1-3)Gal(b1-4)Glc(b1-
#> [9] Fuc(a1-2)Gal(b1-3)GlcNAc(b1-3)Gal(b1-4)Glc(b1-
#> [10] Fuc(a1-3)[Gal(b1-4)]GlcNAc(b1-
#> ... (1761 more not shown)
#> # Unique structures: 1771
glydb_structures(glycan_type = "N")
#> <glydb_structure[3744]>
#> [1] Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-
#> [2] {Neu5Ac(a2-3)Gal(b1-4)GlcNAc(b1-2)}Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-
#> [3] {Neu5Ac(a2-3)}Gal(b1-4)GlcNAc(b1-2)Man(a1-3)[Gal(b1-4)GlcNAc(b1-2)[Gal(b1-4)GlcNAc(b1-6)]Man(a1-6)]Man(b1-4)GlcNAc(b1-4)[Fuc(a1-6)]GlcNAc(b1-
#> [4] GlcNAc(b1-2)[GlcNAc(b1-4)]Man(a1-3)[GlcNAc(b1-2)[GlcNAc(b1-6)]Man(a1-6)]Man(b1-4)GlcNAc(b1-4)[Fuc(a1-6)]GlcNAc(b1-
#> [5] GalNAc(b1-4)GlcNAc(b1-2)Man(a1-3)[GlcNAc(b1-4)GlcNAc(b1-2)Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-
#> [6] Man(a1-3)Man(a1-6)[Man(a1-3)]Man(b1-4)GlcNAc(a1-
#> [7] Fuc(a1-3)[Gal(b1-4)]GlcNAc(b1-4)Man(a1-3)Man(b1-4)GlcNAc(b1-4)[Fuc(a1-6)]GlcNAc(b1-
#> [8] Neu5Ac(a2-3)Gal(b1-3)[Neu5Ac(a2-6)]GlcNAc(b1-2)Man(a1-3)[Neu5Ac(a2-3)Gal(b1-3)GlcNAc(b1-2)Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-
#> [9] Man(a1-2)Man(a1-2)Man(a1-6)[Man(a1-2)Man(a1-3)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-
#> [10] Man(a1-2)Man(a1-3)[GlcNAc(b1-4)][Man(a1-3)[Man(a1-6)]Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(a1-
#> ... (3734 more not shown)
#> # Unique structures: 3744
glydb_structures(glycan_type = "N", mono_range = list(Hex = c(5L, 10L)))
#> <glydb_structure[0]>
#> # Unique structures: 0
glydb_structures(mono_range = list(Hex = c(3L, 9L), HexNAc = c(2L, 6L)))
#> <glydb_structure[1177]>
#> [1] GlcNAc(a1-3)GalNAc(b1-3)Gal(a1-4)Gal(b1-4)Glc(b1-
#> [2] GalNAc(b1-4)GlcNAc(b1-2)Man(a1-3)[GlcNAc(b1-4)GlcNAc(b1-2)Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-
#> [3] Man(a1-2)Man(a1-2)Man(a1-6)[Man(a1-2)Man(a1-3)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-
#> [4] Man(a1-2)Man(a1-3)[GlcNAc(b1-4)][Man(a1-3)[Man(a1-6)]Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(a1-
#> [5] Man(a1-3)Man(a1-6)[Man(b1-3)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-
#> [6] {Gal(b1-4)|3,4,6,7,8}{Gal(b1-4)|3,4,6,7,8}GlcNAc(b1-2)[GlcNAc(b1-4)]Man(a1-3)[GlcNAc(b1-2)Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-
#> [7] Gal(b1-4)GlcNAc(b1-3)[Gal(b1-4)GlcNAc(b1-6)]Gal(b1-4)GlcNAc(b1-3)[Gal(b1-4)GlcNAc(b1-6)]Gal(b1-4)GlcNAc(b1-
#> [8] Man(a1-2)Man(a1-3)[Man(a1-3)[Man(a1-6)]Man(a1-6)]Man(a1-4)GlcNAc(b1-4)GlcNAc(b1-
#> [9] Man(a1-6)Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-
#> [10] Man(a1-4)Man(a1-4)Man(a1-3)[Man(a1-4)Man(a1-3)[Man(a1-4)Man(a1-6)]Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-
#> ... (1167 more not shown)
#> # Unique structures: 1177