Get the Structures or Alignments of Known Motifs

get_motif_structure() and get_motif_alignment() were deprecated in glymotif 0.16.0. Use db_motif_info() to inspect database motifs instead.

Usage

get_motif_structure(name)

get_motif_alignment(name)

Arguments

name

A character vector of motif names.

Value

• get_motif_structure(): a glyrepr::glycan_structure() vector.

• get_motif_alignment(): a character vector of motif alignments.

For get_motif_alignment(), if name has length greater than 1, the return value is named with the motif names.

See also

db_motif_info()

Examples

get_motif_structure("N-Glycan core basic")
#> Warning: `get_motif_structure()` was deprecated in glymotif 0.16.0.
#> ℹ Please use `db_motif_info()` instead.
#> <glycan_structure[1]>
#> [1] Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(?1-
#> # Unique structures: 1
get_motif_alignment("N-Glycan core basic")
#> Warning: `get_motif_alignment()` was deprecated in glymotif 0.16.0.
#> ℹ Please use `db_motif_info()` instead.
#> [1] "core"

get_motif_structure(c("O-Glycan core 1", "O-Glycan core 2"))
#> <glycan_structure[2]>
#> [1] Gal(b1-3)GalNAc(a1-
#> [2] Gal(b1-3)[GlcNAc(b1-6)]GalNAc(a1-
#> # Unique structures: 2
get_motif_alignment(c("O-Glycan core 1", "O-Glycan core 2"))
#> O-Glycan core 1 O-Glycan core 2 
#>          "core"          "core"