Extract the First Structural Match

Extract the first matching fragment from each glycan.

Usage

rex_extract(glycans, pattern)

Arguments

glycans

A character vector of glycan expressions in any format supported by glyparse::auto_parse(), a glyrepr_structure vector, or one glyrepr-compatible igraph. Character inputs may mix formats; malformed structures throw an error.

pattern

A character vector of patterns or one rex_compile() object. Inputs recycle only from length one. Missing glycans or patterns propagate.

Value

A character vector of canonical glyrepr IUPAC strings for character input, or a glyrepr structure vector for structure or graph input. No match or missing input returns a missing value. A cut fragment retains the anomer and donor position of its former attachment linkage.

Details

The matching unit is a connected structural trace. As in glycowork, the first successful trace per starting node is retained, then strict subsets of other traces are removed. Distinct branches with equal sequences remain distinct matches. Matches are ordered by decreasing residue count and then starting node ID. Repeats are greedy unless marked lazy; successful traces may overlap. Counts therefore need not equal text-regex counts. Only connected rooted trees are supported; floating topology or floating substituents are rejected explicitly. See rex_compile() for syntax.

See also

Other glycan queries: rex_count(), rex_detect(), rex_extract_all(), rex_locate(), rex_locate_all(), rex_match(), rex_match_all(), rex_subset(), rex_which()

Examples

x <- c("Gal(b1-4)GlcNAc", "Fuc(a1-3)GlcNAc", NA)
rex_extract(x, "HexNAc")
#> [1] "GlcNAc(?1-" "GlcNAc(?1-" NA