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Locate All Structural Matches

rex_locate_all.Rd

Locate the nodes and edges of all matches in each glycan.

Usage

rex_locate_all(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 list of data frames with integer list-columns nodes and edges. No match produces zero rows; missing input produces one row with NA_integer_ in both columns. IDs are one-based and refer to the input graph, or the canonical graph obtained from character input, as in glyrepr::structure_nodes() and glyrepr::structure_edges(). Only edges within the match are returned.

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_match(), rex_match_all(), rex_subset(), rex_which()

Examples

x <- c("Gal(b1-4)GlcNAc", "Fuc(a1-3)GlcNAc", NA)
rex_locate_all(x, "Gal-GlcNAc")
#> [[1]]
#>   nodes edges
#> 1  1, 2     1
#> 
#> [[2]]
#> [1] nodes edges
#> <0 rows> (or 0-length row.names)
#> 
#> [[3]]
#>   nodes edges
#> 1    NA    NA
#>