Get the Number of Monosaccharides — count

When mono is:

NULL (default), returns the total number of monosaccharides and substituents.
A string, returns the number of the specified monosaccharide or substituent.

Usage

count_mono(x, mono = NULL, include_subs = FALSE)

# S3 method for class 'glyrepr_composition'
count_mono(x, mono = NULL, include_subs = FALSE)

# S3 method for class 'glyrepr_structure'
count_mono(x, mono = NULL, include_subs = FALSE)

Arguments

x: A glycan composition (glyrepr_composition) or a glycan structure (glyrepr_structure) vector.
mono: The monosaccharide or substituent to count. A character scalar. If NULL (default), return the total number of monosaccharides.
include_subs: Whether to include substituents when mono is NULL. Default is FALSE.

Value

A numeric vector of the same length as x.

Details

When mono is "generic" (e.g. "Hex", "HexNAc"), it counts all "concrete" monosaccharides that match. For example, "Hex" will count all Glc, Man, Gal, etc. When mono is "concrete" (e.g. "Gal", "GalNAc"), NA is returned when the composition is "generic".

Examples

comp <- glycan_composition(c(Hex = 5, HexNAc = 2), c(Gal = 1, Man = 1, GalNAc = 1))
count_mono(comp, "Hex")
#> [1] 5 2
count_mono(comp, "Gal")
#> [1] NA  1

struct <- as_glycan_structure("Gal(b1-3)GlcNAc(b1-4)Glc(a1-")
count_mono(struct, "Gal")
#> [1] 1

# Total number of monosaccharides
count_mono(comp)
#> [1] 7 3