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Convert Glycan Structures to Graph Tables

Source: R/structure-tables.R
structure_tables.Rd

structure_nodes() and structure_edges() convert a glycan structure vector to node and edge tibbles. structure_from_tibbles() rebuilds a glyrepr_structure vector from those tibbles and a vector of reducing-end anomers.

The glycan_id column is the integer position of each glycan in the input vector. Duplicate structures are expanded to their original vector positions. Missing structures have no node or edge rows and are reconstructed from missing values in anomers. If x is named, the node and edge tibbles also contain a glycan_name column. structure_from_tibbles() uses glycan_name as output names when that column is present.

Usage

structure_nodes(x)

structure_edges(x)

structure_from_tibbles(nodes, edges, anomers)

Arguments

x

A glycan structure vector.

nodes

A data frame with columns glycan_id, node_id, mono, and sub, and optionally glycan_name.

edges

A data frame with columns glycan_id, edge_id, from_node, to_node, and linkage, and optionally glycan_name.

anomers

A character vector of reducing-end anomers, one per glycan.

Value

  • structure_nodes() returns a tibble with columns glycan_id, node_id, mono, and sub.

  • structure_edges() returns a tibble with columns glycan_id, edge_id, from_node, to_node, and linkage.

  • structure_from_tibbles() returns a glyrepr_structure vector.

Examples

glycans <- c(o_glycan_core_1(), o_glycan_core_1())
nodes <- structure_nodes(glycans)
edges <- structure_edges(glycans)
structure_from_tibbles(nodes, edges, get_anomer(glycans))
#> <glycan_structure[2]>
#> [1] Gal(b1-3)GalNAc(a1-
#> [2] Gal(b1-3)GalNAc(a1-
#> # Unique structures: 1