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,
  mono_range = 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.
mono_range: A named list for filtering compositions 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_composition() 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_compositions()
#> <glycan_composition[1070]>
#> [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)
#> ... (1060 more not shown)
glydb_compositions(mono_type = "generic")
#> <glycan_composition[652]>
#> [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)
#> ... (642 more not shown)
glydb_compositions(species = "Homo sapiens")
#> <glycan_composition[536]>
#> [1] Glc(4)
#> [2] Man(3)GlcNAc(1)
#> [3] Gal(1)GalNAc(1)
#> [4] Gal(1)GlcNAc(1)GalNAc(1)
#> [5] GlcNAc(1)GalNAc(1)
#> [6] GlcNAc(2)GalNAc(1)
#> [7] GalNAc(2)
#> [8] Gal(1)GlcNAc(1)Fuc(2)
#> [9] Glc(1)Gal(2)GlcNAc(1)
#> [10] Glc(1)Gal(2)GlcNAc(1)Fuc(1)
#> ... (526 more not shown)
glydb_compositions(glycan_type = "N")
#> <glycan_composition[473]>
#> [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(6)GlcNAc(3)
#> [6] Man(3)Gal(3)GlcNAc(5)Fuc(1)Neu5Gc(1)
#> [7] Man(2)GlcNAc(2)Fuc(1)
#> [8] Man(3)Gal(3)GlcNAc(5)Neu5Ac(2)
#> [9] Man(2)GlcNAc(3)
#> [10] Man(3)GlcNAc(7)Fuc(1)
#> ... (463 more not shown)
glydb_compositions(glycan_type = "N", mono_range = list(Hex = c(5L, 10L)))
#> <glycan_composition[0]>
glydb_compositions(mono_range = list(Hex = c(3L, 9L), HexNAc = c(2L, 6L)))
#> <glycan_composition[105]>
#> [1] Glc(1)Gal(2)GlcNAc(1)GalNAc(1)
#> [2] Man(6)GlcNAc(2)
#> [3] Man(6)GlcNAc(3)
#> [4] Man(4)GlcNAc(2)
#> [5] Gal(5)GlcNAc(5)
#> [6] Glc(1)Man(8)GlcNAc(2)
#> [7] Man(3)Gal(2)GlcNAc(4)
#> [8] Man(2)Gal(2)GlcNAc(2)
#> [9] Man(3)GlcNAc(5)
#> [10] Gal(4)GlcNAc(3)GalNAc(1)
#> ... (95 more not shown)