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Create a Glycan Structure Vector

Source: R/structure.R
glycan_structure.Rd

glycan_structure() creates an efficient glycan structure vector for storing and processing glycan molecular structures. The function employs hash-based deduplication mechanisms, making it suitable for glycoproteomics, glycomics analysis, and glycan structure comparison studies.

Usage

glycan_structure(...)

is_glycan_structure(x)

Arguments

...

igraph graph objects to be converted to glycan structures, or existing glycan structure vectors. Supports mixed input of multiple objects.

x

An object to check or convert.

Value

A glyrepr_structure class glycan structure vector object.

Data Structure Overview

A glycan structure vector is a vctrs vector with an additional S3 class glyrepr_structure.

Each glycan structure must satisfy the following constraints:

Graph Structure Requirements

  • Must be a directed graph with an outward tree structure (reducing end as root)

  • Must have a graph attribute anomer in the format "a1" or "b1"

    • Unknown parts can be represented with "?", e.g., "?1", "a?", "??"

Node Attributes

  • mono: Monosaccharide names, must be known monosaccharide types

    • Generic names: Hex, HexNAc, dHex, NeuAc, etc.

    • Concrete names: Glc, Gal, Man, GlcNAc, etc.

    • Cannot mix generic and concrete names

    • NA values are not allowed

  • sub: Substituent information

    • Single substituent format: "xY" (x = position, Y = substituent name), e.g., "2Ac", "3S"

    • Multiple substituents separated by commas and ordered by position, e.g., "3Me,4Ac", "2S,6P"

    • Unknown substituent positions can be repeated, e.g., "?Me,?S"

    • No substituents represented by empty string ""

Edge Attributes

  • linkage: Glycosidic linkage information in format "a/bX-Y"

    • Standard format: e.g., "b1-4", "a2-3"

    • Unknown positions allowed: "a1-?", "b?-3", "??-?"

    • Partially unknown positions: "a1-3/6", "a1-3/6/9"

    • NA values are not allowed

Node and Edge Order

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 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".

NA Support

Glycan structure vectors support NA values for representing missing or unknown structures:

  • Create with glycan_structure(NA) or glycan_structure(NULL)

  • Combine with valid structures: c(struct1, NA, struct2)

  • Convert from character: as_glycan_structure(c("Glc(a1-", NA))

  • smap functions skip NA elements gracefully

  • is.na() returns TRUE for NA elements

Naming Support

Glycan structure vectors can have names, which are preserved during operations. This is particularly useful when working with the glymotif package.

Character conversion

A glycan structure vector is not a character vector. Use as.character() to explicitly convert it to IUPAC-condensed strings when needed.

Examples

library(igraph)

# Example 1: Create a simple glycan structure GlcNAc(b1-4)GlcNAc
graph <- make_graph(~ 1-+2)  # Create graph with two monosaccharides
V(graph)$mono <- c("GlcNAc", "GlcNAc")  # Set monosaccharide types
V(graph)$sub <- ""  # No substituents
E(graph)$linkage <- "b1-4"  # b1-4 glycosidic linkage
graph$anomer <- "a1"  # a anomeric carbon

# Create glycan structure vector
simple_struct <- glycan_structure(graph)
print(simple_struct)
#> <glycan_structure[1]>
#> [1] GlcNAc(b1-4)GlcNAc(a1-
#> # Unique structures: 1

# Example 2: Use predefined glycan core structures
n_core <- n_glycan_core()  # N-glycan core structure
o_core1 <- o_glycan_core_1()  # O-glycan Core 1 structure

# Example 3: Create complex structure with substituents
complex_graph <- make_graph(~ 1-+2-+3)
V(complex_graph)$mono <- c("GlcNAc", "Gal", "Neu5Ac")
V(complex_graph)$sub <- c("", "", "")  # Add substituents as needed
E(complex_graph)$linkage <- c("b1-4", "a2-3")
complex_graph$anomer <- "b1"

complex_struct <- glycan_structure(complex_graph)
print(complex_struct)
#> <glycan_structure[1]>
#> [1] Neu5Ac(a2-3)Gal(b1-4)GlcNAc(b1-
#> # Unique structures: 1

# Example 4: Check if object is a glycan structure
is_glycan_structure(simple_struct)  # TRUE
#> [1] TRUE
is_glycan_structure(graph)          # FALSE
#> [1] FALSE