Find Indices of Glycans with Structural Matches

Return the indices of glycans that match a structural pattern.

Usage

rex_which(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

An integer vector of matching input indices. Missing results are omitted. The pattern must have length one or the length of glycans.

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(), rex_extract_all(), rex_locate(), rex_locate_all(), rex_match(), rex_match_all(), rex_subset()

Examples

x <- c("Gal(b1-4)GlcNAc", "Fuc(a1-3)GlcNAc", NA)
rex_which(x, "Fuc")
#> [1] 2
rex_which(x, "Gal", negate = TRUE)
#> [1] 2