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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
)

Arguments

structure_level

Either "intact", "topological", or "basic". 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 "N", "O-GalNAc", "O-GlcNAc", "O-Man", "O-Fuc", "O-Glc". 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.

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.

Note that the confidence attribute will be lost after any vector operation like subsetting. Therefore, if used with glyanno, the returned value should not be modified manually.

Examples

glydb_structures()
#> <glycan_structure[7125]>
#> [1] Glc(b1-3)Glc(b1-3)Glc(b1-
#> [2] Glc(b1-4)Glc(b1-4)Glc(b1-4)Glc(b1-
#> [3] Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-
#> [4] Fuc(a1-2)[GalNAc(a1-3)]Gal(b1-4)GlcNAc(b1-3)[Neu5Gc(a2-6)]GalNAc(a1-
#> [5] Gal(b1-3)GalNAc(a1-
#> [6] Gal(b1-3)[GlcNAc(b1-6)]GalNAc(a1-
#> [7] GlcNAc(b1-3)GalNAc(a1-
#> [8] GlcNAc(b1-3)[GlcNAc(b1-6)]GalNAc(a1-
#> [9] GalNAc(a1-3)GalNAc(a1-
#> [10] GlcNAc(b1-6)GalNAc(a1-
#> ... (7115 more not shown)
#> # Unique structures: 7125
glydb_structures(structure_level = "topological")
#> <glycan_structure[2691]>
#> [1] Glc(??-?)Glc(??-?)Glc(??-
#> [2] Glc(??-?)Glc(??-?)Glc(??-?)Glc(??-
#> [3] Man(??-?)[Man(??-?)]Man(??-?)GlcNAc(??-
#> [4] GalNAc(??-?)[Fuc(??-?)]Gal(??-?)GlcNAc(??-?)[Neu5Gc(??-?)]GalNAc(??-
#> [5] Gal(??-?)GalNAc(??-
#> [6] GlcNAc(??-?)[Gal(??-?)]GalNAc(??-
#> [7] GlcNAc(??-?)GalNAc(??-
#> [8] GlcNAc(??-?)[GlcNAc(??-?)]GalNAc(??-
#> [9] GalNAc(??-?)GalNAc(??-
#> [10] Fuc(??-?)Gal(??-?)[Fuc(??-?)]GlcNAc(??-
#> ... (2681 more not shown)
#> # Unique structures: 2691
glydb_structures(structure_level = "basic")
#> <glycan_structure[2292]>
#> [1] Hex(??-?)Hex(??-?)Hex(??-
#> [2] Hex(??-?)Hex(??-?)Hex(??-?)Hex(??-
#> [3] Hex(??-?)[Hex(??-?)]Hex(??-?)HexNAc(??-
#> [4] HexNAc(??-?)[dHex(??-?)]Hex(??-?)HexNAc(??-?)[NeuGc(??-?)]HexNAc(??-
#> [5] Hex(??-?)HexNAc(??-
#> [6] HexNAc(??-?)[Hex(??-?)]HexNAc(??-
#> [7] HexNAc(??-?)HexNAc(??-
#> [8] HexNAc(??-?)[HexNAc(??-?)]HexNAc(??-
#> [9] dHex(??-?)Hex(??-?)[dHex(??-?)]HexNAc(??-
#> [10] Hex(??-?)HexNAc(??-?)Hex(??-?)Hex(??-
#> ... (2282 more not shown)
#> # Unique structures: 2292
glydb_structures(species = "Homo sapiens")
#> <glycan_structure[1367]>
#> [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-
#> ... (1357 more not shown)
#> # Unique structures: 1367
glydb_structures(glycan_type = "N")
#> <glycan_structure[2609]>
#> [1] 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-
#> [2] Fuc(a1-3)[Gal(b1-4)]GlcNAc(b1-4)Man(a1-3)Man(b1-4)GlcNAc(b1-4)[Fuc(a1-6)]GlcNAc(b1-
#> [3] 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-
#> [4] Man(a1-2)Man(a1-2)Man(a1-6)[Man(a1-2)Man(a1-3)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-
#> [5] Neu5Gc(a2-3)Gal(b1-4)GlcNAc(b1-4)[Gal(b1-4)GlcNAc(b1-2)]Man(a1-3)[Gal(b1-4)GlcNAc(b1-2)Man(a1-6)]Man(b1-4)GlcNAc(b1-4)[Fuc(a1-6)]GlcNAc(b1-
#> [6] Man(a1-6)Man(b1-4)GlcNAc(b1-4)[Fuc(a1-6)]GlcNAc(b1-
#> [7] Neu5Ac(a2-6)Gal(b1-4)GlcNAc(b1-2)[Neu5Ac(a2-6)Gal(b1-4)GlcNAc(b1-4)]Man(a1-3)[Gal(b1-4)GlcNAc(b1-2)Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-
#> [8] GlcNAc(b1-3)Man(a1-6)Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-
#> [9] GlcNAc(b1-2)[GlcNAc(b1-6)]Man(a1-3)[GlcNAc(b1-4)][GlcNAc(b1-2)[GlcNAc(b1-4)]Man(a1-6)]Man(b1-4)GlcNAc(b1-4)[Fuc(a1-6)]GlcNAc(b1-
#> [10] GlcNAc(b1-2)[GlcNAc(b1-4)]Man(a1-3)[GlcNAc(b1-2)[GlcNAc(b1-4)]Man(a1-6)]Man(b1-4)GlcNAc(b1-4)[Fuc(a1-3)]GlcNAc(b1-
#> ... (2599 more not shown)
#> # Unique structures: 2609
glydb_structures(glycan_type = "N", mono_range = list(Hex = c(5L, 10L)))
#> <glycan_structure[0]>
#> # Unique structures: 0
glydb_structures(mono_range = list(Hex = c(3L, 9L), HexNAc = c(2L, 6L)))
#> <glycan_structure[1031]>
#> [1] GlcNAc(a1-3)GalNAc(b1-3)Gal(a1-4)Gal(b1-4)Glc(b1-
#> [2] Man(a1-2)Man(a1-2)Man(a1-6)[Man(a1-2)Man(a1-3)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-
#> [3] 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-
#> [4] Man(a1-3)Man(a1-6)[Man(b1-3)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-
#> [5] 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-
#> [6] Man(a1-2)Man(a1-3)[Man(a1-3)[Man(a1-6)]Man(a1-6)]Man(a1-4)GlcNAc(b1-4)GlcNAc(b1-
#> [7] Man(a1-6)Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-
#> [8] 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-
#> [9] Glc(b1-3)Man(a1-2)Man(a1-2)Man(a1-3)[Man(a1-2)Man(a1-6)[Man(a1-3)]Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-
#> [10] Gal(b1-4)GlcNAc(b1-4)Man(a1-3)[Gal(b1-4)GlcNAc(b1-4)Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-
#> ... (1021 more not shown)
#> # Unique structures: 1031