Detect Structural Matches in Glycans

Test whether each glycan contains a structural pattern.

Usage

rex_detect(glycans, pattern, negate = FALSE)

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.

negate

Invert detection when TRUE; missing values remain missing.

Value

A logical vector. Missing glycans or patterns return NA.

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_extract(), 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_detect(x, "Gal-HexNAc")
#> [1]  TRUE FALSE    NA
rex_detect(x, "Gal", negate = TRUE)
#> [1] FALSE  TRUE    NA