Compute glycan traits from a parsed glycan tree — compute_glycan

Combine residue-level composition traits (see count_residues), structural traits (see compute_structural_traits), and user-defined motifs (see compute_userdefined_traits) into a unified trait vector.

compute_glycan_traits(tree, motifs = NULL)

Arguments

tree: A parsed glycan tree from pGlyco3_to_tree or wurcs_to_tree.
motifs: Optional named list of user-defined glycan motifs.

Value

A named list of numeric trait values.

Examples

# Example: parse a pGlyco3-style glycan expression into a tree
pGlyco_expr <- "(N(N(H(H(H))(H(H)(H)(H(H))))))"

# Convert to glycan tree structure
tree <- pGlyco3_to_tree(pGlyco_expr)

# Explore parsed nodes and edges
tree$node
#>  [1] "N" "N" "H" "H" "H" "H" "H" "H" "H" "H"
tree$edge
#> [1] "a-b" "b-c" "c-d" "d-e" "c-f" "f-g" "f-h" "f-i" "i-j"

# Build igraph representation
g <- build_glycan_igraph(tree)
plot_glycan_tree(g)


# Define user motifs for trait computation
user_motifs <- list(
  LinearH3 = list(
    node = c("H", "H", "H"),
    edge = c("a-b", "b-c")
  ),
  FucBranch = list(
    node = c("H", "N", "F"),
    edge = c("a-b", "b-c")
  )
)

# Compute glycan structural traits
compute_glycan_traits(tree, motifs = user_motifs)
#> $GlycanSize
#> [1] 10
#> 
#> $Hexose
#> [1] 8
#> 
#> $HexNAc
#> [1] 2
#> 
#> $Neu5Ac
#> [1] 0
#> 
#> $Neu5Gc
#> [1] 0
#> 
#> $Fucose
#> [1] 0
#> 
#> $Antennas
#> [1] 0
#> 
#> $IsBisecting
#> [1] 0
#> 
#> $IsComplex
#> [1] 0
#> 
#> $IsOligomannose
#> [1] 1
#> 
#> $IsHybrid
#> [1] 0
#> 
#> $IsC_Fucosed
#> [1] 0
#> 
#> $IsA_Fucosed
#> [1] 0
#> 
#> $LinearH3
#> [1] 5
#> 
#> $FucBranch
#> [1] 0
#>