Convert to Glycan Structure Vector — as_glycan

Convert an object to a glycan structure vector.

Usage

as_glycan_structure(x, on_failure = c("error", "na"))

Arguments

x: An object to convert to a glycan structure vector. Can be an igraph object, a list of igraph objects, a character vector of IUPAC-condensed strings, or an existing glyrepr_structure object.
on_failure: The failure policy for element-local parsing, validation, and canonicalization errors. "error" preserves the default strict behavior. "na" replaces failed elements with NA and emits one warning that reports their positions and failure reasons. Existing missing elements remain missing without a warning. Vector-level incompatibilities still produce an error.

Value

A glyrepr_structure object.

Examples

library(igraph)
#> 
#> Attaching package: ‘igraph’
#> The following objects are masked from ‘package:stats’:
#> 
#>     decompose, spectrum
#> The following object is masked from ‘package:base’:
#> 
#>     union

# Convert a single igraph
graph <- make_graph(~ 1-+2)
V(graph)$mono <- c("GlcNAc", "GlcNAc")
V(graph)$sub <- ""
E(graph)$linkage <- "b1-4"
graph$anomer <- "a1"
as_glycan_structure(graph)
#> <glycan_structure[1]>
#> [1] GlcNAc(b1-4)GlcNAc(a1-
#> # Unique structures: 1

# Convert a list of igraphs
o_glycan_vec <- o_glycan_core_1()
o_glycan_graph <- get_structure_graphs(o_glycan_vec)
as_glycan_structure(list(graph, o_glycan_graph))
#> <glycan_structure[2]>
#> [1] GlcNAc(b1-4)GlcNAc(a1-
#> [2] Gal(b1-3)GalNAc(a1-
#> # Unique structures: 2

# Convert a character vector of IUPAC-condensed strings
as_glycan_structure(c("GlcNAc(b1-4)GlcNAc(b1-", "Man(a1-2)GlcNAc(b1-"))
#> <glycan_structure[2]>
#> [1] GlcNAc(b1-4)GlcNAc(b1-
#> [2] Man(a1-2)GlcNAc(b1-
#> # Unique structures: 2

# Preserve valid elements while replacing an invalid element with NA
as_glycan_structure(
  c(valid = "Glc(?1-", invalid = "not-a-structure"),
  on_failure = "na"
)
#> Warning: 1 structure failed validation and was replaced with `NA`.
#> ✖ Position 2 (`invalid`): Could not parse IUPAC-condensed string:
#>   "not-a-structure" ℹ Can't extract anomer information. ℹ Anomer information is
#>   required for the reducing-end monosaccharide. ℹ For example, use 'Man(a1-'
#>   instead of 'Man'.
#> <glycan_structure[2]>
#> [1] valid	Glc(?1-
#> [2] invalid	NA
#> # Unique structures: 1