Skip to contents

Match Motif(s) in Glycans

Source: R/match-motif.R
match_motif.Rd

These functions find all occurrences of the given motif(s) in the glycans. Node-to-node mapping is returned for each match. This function is NOT useful for most users if you are not interested in the concrete node mapping. See have_motif() and count_motif() for more information about the matching rules.

  • match_motif() matches a single motif against multiple glycans

  • match_motifs() matches multiple motifs against multiple glycans

Different from have_motif() and count_motif(), these functions return detailed match information. More specifically, for each glycan-motif pair, a integer vector is returned, indicating the node mapping from the motif to the glycan. For example, if the vector is c(2, 3, 6), it means that the first node in the motif matches the 2nd node in the glycan, the second node in the motif matches the 3rd node in the glycan, and the third node in the motif matches the 6th node in the glycan.

Node indices are only meaningful for glyrepr::glycan_structure(), so only glyrepr::glycan_structure() is supported for glycans and motifs.

Usage

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

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

Arguments

glycans

One of:

motif

One of:

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:

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

A nested list of integer vectors.

  • match_motif(): Two levels of nesting. The outer list corresponds to glycans, and the inner list corresponds to matches. Use purrr::pluck(result, glycan_index, match_index) to access the match information. For example, purrr::pluck(result, 1, 2) means the 2nd match in the 1st glycan.

  • match_motifs(): Three levels of nesting. The outermost list corresponds to motifs, the middle list corresponds to glycans, and the innermost list corresponds to matches. Use purrr::pluck(result, motif_index, glycan_index, match_index) to access the match information. For example, purrr::pluck(result, 1, 2, 3) means the 3rd match in the 2nd glycan for the 1st motif. The outermost list is named by motifs if they have names. The middle list is named by glycans if they have names.

Vertex and Linkage Indices

The indices of vertices and linkages in a glycan correspond directly to their order in the IUPAC-condensed string, which is printed when you print a glyrepr::glycan_structure(). For example, for the glycan Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-), the vertices are "Man", "Man", "Man", "GlcNAc", "GlcNAc", and the linkages are "a1-3", "a1-6", "b1-4", "b1-4".

Thus, matching the motif "Man(a1-3)Man(b1-4)" to this glycan yields c(1, 3). This indicates that the first motif vertex (the a1-3 Man) corresponds to the first vertex in the glycan, and the second motif vertex (the b1-4 Man) corresponds to the third vertex in the glycan.

About Names

match_motif() perserve names from the input glycans vector.`

For match_motifs(), the outermost list is named by motifs, and the inner lists are named by glycans, following the same rules as in have_motifs() and count_motifs().

See also

have_motif(), count_motif()

Examples

library(glyparse)
library(glyrepr)

(glycan <- n_glycan_core())
#> <glycan_structure[1]>
#> [1] Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-
#> # Unique structures: 1

# Let's peek under the hood of the nodes in the glycan
glycan_graph <- get_structure_graphs(glycan)
igraph::V(glycan_graph)$mono # 1, 2, 3, 4, 5
#> [1] "Man"    "Man"    "Man"    "GlcNAc" "GlcNAc"

# Match a single motif against a single glycan
motif <- parse_iupac_condensed("Man(a1-3)[Man(a1-6)]Man(b1-")
match_motif(glycan, motif)
#> [[1]]
#> [[1]][[1]]
#> [1] 1 2 3
#> 
#> 

# Match multiple motifs against a single glycan
motifs <- c(
  "Man(a1-3)[Man(a1-6)]Man(b1-",
  "Man(a1-3)Man(b1-4)GlcNAc(b1-4)GlcNAc(?1-"
)
motifs <- parse_iupac_condensed(motifs)
match_motifs(glycan, motifs)
#> [[1]]
#> [[1]][[1]]
#> [[1]][[1]][[1]]
#> [1] 1 2 3
#> 
#> 
#> 
#> [[2]]
#> [[2]][[1]]
#> [[2]][[1]][[1]]
#> [1] 1 3 4 5
#> 
#> 
#>