Extract Branch Motifs — extract_branch

An N-glycan branching motif if the substructures linked to either the a3- or a6-core-mannose.

For example:

Neu5Ac - Gal - GlcNAc - Man
~~~~~~~~~~~~~~~~~~~~~      \
  A branching motif         Man - GlcNAc - GlcNAc -
                           /
                        Man

This function returns all the unique branching motifs found in the input glycans.

If you want to perform branching motif matching in functions like have_motifs() or glydet::quantify_motifs(), use the branch_motifs() helper instead, which handles additional intricacies related to how the motifs should be matched.

Usage

extract_branch_motif(glycans, ..., including_core = FALSE)

Arguments

glycans

One of:

A glyrepr::glycan_structure() vector.
A glycan structure string vector. All formats supported by glyparse::auto_parse() are accepted.

...

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

including_core

A logical scalar. If TRUE, the N-glycan core structure (Man(??-?)Man(??-?)GlcNAc(??-?)GlcNAc(??- or Hex(??-?)Hex(??-?)HexNAc(??-?)HexNAc(??-) is appended to each branch motif. Concrete branches receive a concrete core; generic and mixed branches receive a generic core. Default is FALSE.

Value

A glyrepr::glycan_structure() vector containing the unique extracted branching motifs.

Details

The function works by:

Converting the input to a set of unique glycan_structure objects.
Searching for the N-glycan branch pattern: HexNAc(??-?)Hex(??-?)Hex(??-?)HexNAc(??-?)HexNAc(??-.
For each match, identifying the root node of the branch (the leftmost HexNAc in the pattern).
Extracting the full subtree rooted at that node.
Preserving the correct anomeric configuration (e.g., "b1") by inspecting the linkage to the root node.

Examples

glycans <- c(
  "Neu5Ac(a2-3)Gal(b1-4)GlcNAc(b1-2)Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(a1-4)GlcNAc(b1-",
  "Gal(b1-4)GlcNAc(b1-2)Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(a1-4)GlcNAc(b1-"
)
extract_branch_motif(glycans)
#> <glycan_structure[2]>
#> [1] Neu5Ac(a2-3)Gal(b1-4)GlcNAc(b1-
#> [2] Gal(b1-4)GlcNAc(b1-
#> # Unique structures: 2