Count How Many Times Glycans have the Given Motif(s)

These functions are closely related to have_motif(). However, instead of returning logical values, they return the number of times the glycans have the motif(s).

• count_motif() counts a single motif in multiple glycans

• count_motifs() counts multiple motifs in multiple glycans

Usage

count_motif(
  glycans,
  motif,
  alignment = NULL,
  ignore_linkages = FALSE,
  strict_sub = TRUE,
  match_degree = NULL
)

count_motifs(
  glycans,
  motifs,
  alignments = NULL,
  ignore_linkages = FALSE,
  strict_sub = TRUE,
  match_degree = NULL
)

Arguments

glycans

One of:

• A glyrepr::glycan_structure() vector.

• A glycan structure string vector. All formats supported by glyparse::auto_parse() are accepted, including IUPAC-condensed, WURCS, GlycoCT, and others.

motif

One of:

• A glyrepr::glycan_structure() scalar.

• A glycan structure string, supported by glyparse::auto_parse().

• A known motif name (use db_motifs() to see all available motifs).

alignment

A character string. Possible values are "substructure", "core", "terminal", and "whole". If not provided, the value will be decided based on the motif argument. If motif is a motif name, the alignment in the database will be used. Otherwise, "substructure" will be used.

ignore_linkages

A logical value. If TRUE, linkages will be ignored in the comparison. Default is FALSE.

strict_sub

A logical value. If TRUE (default), substituents will be matched in strict mode, which means if the glycan has a substituent in some residue, the motif must have the same substituent to be matched.

match_degree

A logical vector indicating which motif nodes must match the glycan's in- and out-degree exactly. For have_motif(), count_motif(), and match_motif(), this must be a logical vector with length 1 or the number of motif nodes (length 1 is recycled). For have_motifs(), count_motifs(), and match_motifs(), this must be a list of logical vectors with length equal to motifs; each element follows the same length rules. When match_degree is provided, alignment and alignments are silently ignored.

motifs

One of:

• A glyrepr::glycan_structure() vector.

• A glycan structure string vector, supported by glyparse::auto_parse().

• A character vector of motif names (use db_motifs() to see all available motifs).

alignments

A character vector specifying alignment types for each motif. Can be a single value (applied to all motifs) or a vector of the same length as motifs.

Value

• count_motif(): An integer vector indicating how many times each glycan has the motif.

• count_motifs(): An integer matrix where rows correspond to glycans and columns correspond to motifs. Row names contain glycan identifiers and column names contain motif identifiers.

Details

This function actually perform v2f algorithm to get all possible matches between glycans and motif. However, the result is not necessarily the number of matches.

Think about the following example:

• glycan: Gal(b1-?)[Gal(b1-?)]GlcNAc(b1-4)GlcNAc(b1-

• motif: Gal(b1-?)[Gal(b1-?)]GlcNAc(b1-

To draw the glycan out:

Gal 1
   \ b1-? b1-4
    GlcNAc -- GlcNAc b1-
   / b1-?
Gal 2

To draw the motif out:

Gal 1
   \ b1-?
    GlcNAc b1-
   / b1-?
Gal 2

To differentiate the galactoses, we number them as "Gal 1" and "Gal 2" in both the glycan and the motif. The v2f subisomorphic algorithm will return two matches:

• Gal 1 in the glycan matches Gal 1 in the motif, and Gal 2 matches Gal 2.

• Gal 1 in the glycan matches Gal 2 in the motif, and Gal 2 matches Gal 1.

However, from a biological perspective, the two matches are the same. This function will take care of this, and return the "unique" number of matches.

For other details about the handling of monosaccharide, linkages, alignment, substituents, and implementation, see have_motif().

About Names

have_motif() and count_motif() perserve names from the input glycans vector.

have_motifs() and count_motifs() return a matrix with both row and column names. The row names are the glycan names, and the column names are the motif names.

Glycan names follow the same rule as have_motif() and count_motif().

Motif names have the following rules:

1. If motifs have names, use the names.

2. If motifs don't have names and are known motif names in the database (e.g. "N-glycan core"), use them.

3. Otherwise, no colnames.

See also

have_motif(), have_motifs()

Examples

library(glyparse)

count_motif("Gal(b1-3)Gal(b1-3)GalNAc(b1-", "Gal(b1-")
#> [1] 2
count_motif(
  "Man(b1-?)[Man(b1-?)]GalNAc(b1-4)GlcNAc(b1-",
  "Man(b1-?)[Man(b1-?)]GalNAc(b1-"
)
#> [1] 1
count_motif("Gal(b1-3)Gal(b1-", "Man(b1-")
#> [1] 0

# Vectorized usage with single motif
count_motif(c("Gal(b1-3)Gal(b1-3)GalNAc(b1-", "Gal(b1-3)GalNAc(b1-"), "Gal(b1-")
#> [1] 2 1

# Multiple motifs with count_motifs()
glycan1 <- parse_iupac_condensed("Gal(b1-3)Gal(b1-3)GalNAc(b1-")
glycan2 <- parse_iupac_condensed("Man(b1-?)[Man(b1-?)]GalNAc(b1-4)GlcNAc(b1-")
glycans <- c(glycan1, glycan2)

motifs <- c("Gal(b1-3)GalNAc(b1-", "Gal(b1-", "Man(b1-")
result <- count_motifs(glycans, motifs)
print(result)
#>                                            [,1] [,2] [,3]
#> Gal(b1-3)Gal(b1-3)GalNAc(b1-                  1    2    0
#> Man(b1-?)[Man(b1-?)]GalNAc(b1-4)GlcNAc(b1-    0    0    2

# Monosaccharide type matching examples
# Concrete glycan vs generic motif: matches (glycan converted to generic)
count_motif("Man(?1-", "Hex(?1-") # Returns 1
#> [1] 1

# Generic glycan vs concrete motif: doesn't match
count_motif("Hex(?1-", "Man(?1-") # Returns 0
#> [1] 0