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Low-Level Motif Matching on Graphs

Source: R/g-motif.R
dot-g_motif.Rd

These functions are low-level variants of have_motif(), count_motif(), and match_motif() for package code that already has compatible igraph objects from glyrepr::get_structure_graphs().

Usage

.g_have_motif(
  glycan_graph,
  motif_graph,
  ...,
  alignment = "substructure",
  ignore_linkages = FALSE,
  strict_sub = TRUE,
  match_degree = NULL,
  mode = c("strict", "lenient"),
  strict_floating = TRUE
)

.g_count_motif(
  glycan_graph,
  motif_graph,
  ...,
  alignment = "substructure",
  ignore_linkages = FALSE,
  strict_sub = TRUE,
  match_degree = NULL,
  mode = c("strict", "lenient"),
  strict_floating = TRUE
)

.g_match_motif(
  glycan_graph,
  motif_graph,
  ...,
  alignment = "substructure",
  ignore_linkages = FALSE,
  strict_sub = TRUE,
  match_degree = NULL,
  mode = c("strict", "lenient")
)

Arguments

glycan_graph

An igraph glycan graph.

motif_graph

An igraph motif graph.

...

These dots must be empty and are used only to force optional arguments to be supplied by name.

alignment

A character scalar: "substructure", "core", "terminal", or "whole".

ignore_linkages

A logical scalar. If TRUE, linkages are ignored.

strict_sub

A logical scalar. If TRUE, substituents are matched strictly.

match_degree

A logical vector indicating which motif nodes must match the glycan's in- and out-degree exactly. A scalar is recycled to the number of motif nodes.

mode

Matching mode. "strict" preserves the default behavior; "lenient" treats glycan-side unknowns as compatible with more specific motif fields.

strict_floating

A logical scalar. For .g_have_motif(), TRUE requires the motif in every possible floating localization and FALSE requires it in at least one. For .g_count_motif(), TRUE returns the minimum count across localizations and FALSE returns the maximum.

Value

  • .g_have_motif() returns a logical scalar.

  • .g_count_motif() returns an integer scalar.

  • .g_match_motif() returns a list of integer vectors.

Details

These functions do no validation, parsing, naming, or graph mutation. Callers must provide valid graph objects. Residue compatibility follows the high-level matching rules, including generic and mixed motif residues.

These functions never call glyrepr::as_glycan_structure().

Glycan graphs with unresolved floating parts or substituents are matched across all conflict-free localizations. .g_match_motif() returns the union of mappings from every localization, with node indices referring to the original unresolved graph.

See also

have_motif(), count_motif(), match_motif()

Examples

library(glyparse)
library(glyrepr)

glycan <- parse_iupac_condensed("Gal(b1-3)GalNAc(b1-")
motif <- parse_iupac_condensed("Gal(b1-")
glycan_graph <- get_structure_graphs(glycan)
motif_graph <- get_structure_graphs(motif)

.g_have_motif(glycan_graph, motif_graph)
#> [1] TRUE
.g_count_motif(glycan_graph, motif_graph)
#> [1] 1
.g_match_motif(glycan_graph, motif_graph)
#> [[1]]
#> [1] 1
#>