Constructor for ConsortiumMetabolismAlignment Objects

Builds a valid ConsortiumMetabolismAlignment by constructing a TSE base and setting CMA-specific slots with sensible defaults.

Usage

ConsortiumMetabolismAlignment(..., tse = NULL)

Arguments

...

Named CMA slot values to set (e.g., Type = "pairwise", PrimaryScore = 0.8).

tse

An optional TreeSummarizedExperiment to use as the base. Default creates an empty TSE.

Value

A validated ConsortiumMetabolismAlignment object.

Slots

Name

character. Display name for the alignment.

Description

character. Optional short description.

Type

character. One of "pairwise", "multiple", or "search".

Metric

character. Similarity metric used (e.g., "FOS").

Params

list. Additional parameters passed to the alignment method.

QueryName

character. Name of the query consortium (pairwise).

ReferenceName

character. Name of the reference consortium (pairwise).

Scores

list. Named list of all computed score components.

PrimaryScore

numeric. Primary similarity score, between 0 and 1.

Pvalue

numeric. Permutation p-value, between 0 and 1.

SharedPathways

data.frame. Pathways present in both query and reference.

UniqueQuery

data.frame. Pathways unique to the query.

UniqueReference

data.frame. Pathways unique to the reference.

SimilarityMatrix

matrix. Pairwise similarity matrix (multiple alignment).

ConsensusPathways

data.frame. Consensus network pathways (multiple alignment).

Prevalence

data.frame. Pathway prevalence across consortia (multiple alignment).

Dendrogram

list. Hierarchical clustering dendrogram (multiple alignment).

Pathways

data.frame. Combined pathway list.

Graphs

list. List of igraph objects.

Metabolites

data.frame. Metabolite mapping table.

See also

TreeSummarizedExperiment, align

Examples

# Empty alignment
cma <- ConsortiumMetabolismAlignment()

# Pairwise alignment via align()
cm1 <- synCM("comm_1", n_species = 3, max_met = 5)
cm2 <- synCM("comm_2", n_species = 4, max_met = 6)
cma <- align(cm1, cm2)
cma
#> 
#> ── ConsortiumMetabolismAlignment 
#> Name: NA
#> Type: "pairwise"
#> Metric: "FOS"
#> Score: 0.2727
#> Query: "comm_1", Reference: "comm_2"