Get Monosaccharide Types

This function determines the type of monosaccharides in character vectors, glycan compositions, or glycan structures. Supported types: "concrete" and "generic" (see details below).

Usage

get_mono_type(x)

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

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

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

Arguments

x

Either of these objects:

• A character vector of monosaccharide names;

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

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

Value

A character vector specifying the monosaccharide type(s). For structures and compositions, returns the type for each element.

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.

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

Special monosaccharides

Some monosaccharides are special in that they have no generic names in database or literature. For example, "Mur" is a rare monosaccharide that has no popular generic name. In glyrepr, we assign a "g" prefix to these monosaccharides as their generic names. This includes "gNeu", "gKdn", "gPse", "gLeg", "gAci", "g4eLeg", "gBac", "gKdo", "gMur". These names might only be meaningful inside glycoverse. Take care when you export results from glycoverse functions to other analysis tools.

See also

convert_to_generic()

Examples

# Character vector
get_mono_type(c("Gal", "Hex"))
#> [1] "concrete" "generic" 

# Glycan structures
get_mono_type(n_glycan_core(mono_type = "concrete"))
#> [1] "concrete"
get_mono_type(n_glycan_core(mono_type = "generic"))
#> [1] "generic"

# Glycan compositions
comp <- glycan_composition(c(Glc = 2, GalNAc = 1))
get_mono_type(comp)
#> [1] "concrete"

# Special cases
comps <- glycan_composition(
  c(Neu = 1),
  c(Neu = 1, Glc = 1),
  c(gMur = 1, Hex = 1),
)
get_mono_type(comps)
#> [1] "concrete" "concrete" "generic"