Skip to contents

Convert Monosaccharides to Generic Type

Source: R/mono-type.R
convert_to_generic.Rd

This function converts monosaccharide types of monosaccharide characters, glycan compositions, or glycan structures from concrete to generic type. This is a simplified version that only supports conversion from "concrete" to "generic" monosaccharides.

Usage

convert_to_generic(x)

# S3 method for class 'character'
convert_to_generic(x)

# S3 method for class 'glyrepr_structure'
convert_to_generic(x)

# S3 method for class 'igraph'
convert_to_generic(x)

# S3 method for class 'glyrepr_composition'
convert_to_generic(x)

Arguments

x

Either of these objects:

  • A character of monosaccharide;

  • A glycan composition vector ("glyrepr_composition" object);

  • A glycan structure vector ("glyrepr_structure" object);

  • A glycan igraph.

Value

A new object of the same class as x with monosaccharides converted to generic type. Graph input retains its vertex IDs and order.

Two types of monosaccharides

There are two types of monosaccharides:

  • concrete: e.g. "Gal", "GlcNAc", "Glc", "Fuc", etc.

  • generic: e.g. "Hex", "HexNAc", "HexA", "HexN", etc. Concrete furanose forms such as "Galf" and "GlcfNAc" convert to the same generic names as their ringless forms: "Hex" and "HexNAc", respectively. Explicit unusual configurations also convert to the same generic names as their natural counterparts. For example, "D-Fuc" and "D-Fucf" both convert to "dHex".

For the full list of monosaccharides, use available_monosaccharides().

Examples

# Convert character vectors
convert_to_generic(c("Gal", "GlcNAc", "Galf", "GlcfNAc"))
#> [1] "Hex"    "HexNAc" "Hex"    "HexNAc"

# Convert glycan compositions
comps <- glycan_composition(
  c(Gal = 5, GlcNAc = 2),
  c(Glc = 5, GalNAc = 4, Fuc = 1)
)
convert_to_generic(comps)
#> <glycan_composition[2]>
#> [1] Hex(5)HexNAc(2)
#> [2] Hex(5)HexNAc(4)dHex(1)

# Convert glycan structures
strucs <- c(n_glycan_core(), o_glycan_core_1())
convert_to_generic(strucs)
#> <glycan_structure[2]>
#> [1] Hex(a1-3)[Hex(a1-6)]Hex(b1-4)HexNAc(b1-4)HexNAc(b1-
#> [2] Hex(b1-3)HexNAc(a1-
#> # Unique structures: 2