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Create a Glycan Composition

glycan_composition.Rd

Create a glycan composition from a list of named integer vectors. Compositions can contain both monosaccharides and substituents.

Usage

glycan_composition(...)

is_glycan_composition(x)

Arguments

...

Named integer vectors. Names are monosaccharides or substituents, values are numbers of residues. Monosaccharides and substituents can be mixed in the same composition.

x

A list of named integer vectors.

Value

A glyrepr_composition object.

Details

Compositions can contain:

  • Monosaccharides: either generic (e.g., "Hex", "HexNAc") or concrete (e.g., "Glc", "Gal"). All monosaccharides in a composition must be of the same type.

  • Substituents: e.g., "Me", "Ac", "S". These can be mixed with either generic or concrete monosaccharides.

Components are automatically sorted with monosaccharides first (according to their order in the monosaccharides table), followed by substituents (according to their order in available_substituents()).

See also

available_monosaccharides(), available_substituents()

Examples

# A vector with one composition (generic monosaccharides)
glycan_composition(c(Hex = 5, HexNAc = 2))
#> <glycan_composition[1]>
#> [1] Hex(5)HexNAc(2)
# A vector with multiple compositions
glycan_composition(c(Hex = 5, HexNAc = 2), c(Hex = 5, HexNAc = 4, dHex = 2))
#> <glycan_composition[2]>
#> [1] Hex(5)HexNAc(2)
#> [2] Hex(5)HexNAc(4)dHex(2)
# Residues are reordered automatically
glycan_composition(c(HexNAc = 1, Hex = 2))
#> <glycan_composition[1]>
#> [1] Hex(2)HexNAc(1)
# An example for generic monosaccharides
glycan_composition(c(Hex = 2, HexNAc = 1))
#> <glycan_composition[1]>
#> [1] Hex(2)HexNAc(1)
# An example for concrete monosaccharides
glycan_composition(c(Glc = 2, Gal = 1))
#> <glycan_composition[1]>
#> [1] Glc(2)Gal(1)
# Compositions with substituents
glycan_composition(c(Glc = 1, S = 1))
#> <glycan_composition[1]>
#> [1] Glc(1)S(1)
glycan_composition(c(Hex = 3, HexNAc = 2, Me = 1, Ac = 1))
#> <glycan_composition[1]>
#> [1] Hex(3)HexNAc(2)Me(1)Ac(1)
# Substituents are sorted after monosaccharides
glycan_composition(c(S = 1, Gal = 1, Ac = 1, Glc = 1))
#> <glycan_composition[1]>
#> [1] Glc(1)Gal(1)Ac(1)S(1)