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Subset ramen Objects by Metabolite

Source: R/methods-subset.R
subset-ramen.Rd

Subsetting methods for ramen S4 classes. For ConsortiumMetabolismSet, [ follows the TreeSummarizedExperiment contract: the assays are metabolite x metabolite (m x m), so i and j index the metabolite space, not the consortium list. After subsetting, all custom slots are updated eagerly: BinaryMatrices is subsetted to the remaining metabolite space and OverlapMatrix, Dendrogram, NodeData, Pathways, Metabolites, and Graphs are recomputed accordingly. The per-consortium list returned by consortia() is not modified — each ConsortiumMetabolism retains its own metabolite space.

Note on consortium-level selection: to extract a subset of consortia rather than a subset of the metabolite space, use extractCluster (dendrogram-based) or the planned filterConsortia() method. Metabolite subsetting is appropriate when the analysis should focus on a specific part of the metabolic network — for example, subsetting to the core-pathway metabolites (pathways(cms, type = "core")) to compare consortia on their shared metabolic backbone only.

ConsortiumMetabolism and ConsortiumMetabolismAlignment do not support [ and return an informative error.

Usage

# S4 method for class 'ConsortiumMetabolism,ANY,ANY,ANY'
x[i, j, ..., drop = FALSE]

# S4 method for class 'ConsortiumMetabolismSet,ANY,ANY,ANY'
x[i, j, ..., drop = FALSE]

# S4 method for class 'ConsortiumMetabolismAlignment,ANY,ANY,ANY'
x[i, j, ..., drop = FALSE]

Arguments

x

A ramen S4 object.

i

Row (metabolite) indices — integer, logical, or character names from metabolites(cms).

j

Column indices. Must be identical to i (or omitted): since assays are m x m, asymmetric subsetting is not meaningful.

...

Additional arguments passed to the TSE parent method.

drop

Ignored; retained for S4 signature compatibility.

Value

For ConsortiumMetabolismSet: a subsetted object with all custom slots updated to reflect the remaining metabolite space. For ConsortiumMetabolism and ConsortiumMetabolismAlignment: an error.

Functions

  • x[i: Subsetting a ConsortiumMetabolism is not supported.

  • x[i: Subset a ConsortiumMetabolismSet by metabolite index with full slot synchronisation.

  • x[i: Subsetting a ConsortiumMetabolismAlignment is not supported.

See also

extractCluster for dendrogram-based consortium selection.

Examples

cm1 <- synCM("a", n_species = 3, max_met = 6, seed = 1)
cm2 <- synCM("b", n_species = 3, max_met = 6, seed = 2)
cms <- ConsortiumMetabolismSet(
    cm1, cm2, name = "test", verbose = FALSE
)
## Subset to first 3 metabolites (m x m assay semantics)
sub <- cms[seq_len(3), seq_len(3)]
dim(sub)
#> [1] 3 3