Constructor for ConsortiumMetabolismAlignment Objects

Builds a valid ConsortiumMetabolismAlignment by setting CMA-specific slots with sensible defaults.

Exports alignment results to a plain data.frame suitable for downstream analysis. For "pairwise" alignments the three pathway sets (SharedPathways, UniqueQuery, UniqueReference) are row-bound with a pathway_type column added. For "multiple" alignments ConsensusPathways is returned. For all other types (or empty objects) Pathways is returned, falling back to an empty data.frame().

Usage

ConsortiumMetabolismAlignment(...)

# S4 method for class 'ConsortiumMetabolismAlignment'
as.data.frame(x, row.names = NULL, optional = FALSE, ...)

Arguments

...

Additional arguments (currently unused).

x

A ConsortiumMetabolismAlignment object.

row.names

NULL or a character vector of row names; ignored.

optional

Logical; ignored.

Value

A validated ConsortiumMetabolismAlignment object.

A data.frame. For pairwise alignments the result contains at minimum consumed, produced, and pathway_type columns.

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

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: "comm_1 vs comm_2"
#> Type: "pairwise"
#> Metric: "FOS"
#> Score: 0
#> Query: "comm_1", Reference: "comm_2"
#> Coverage: query 0, reference 0
#> Pathways: 0 shared, 3 query-only, 12 reference-only.

cm1 <- synCM("comm_1", n_species = 3, max_met = 5)
cm2 <- synCM("comm_2", n_species = 4, max_met = 6)
cma <- align(cm1, cm2)
df <- as.data.frame(cma)
head(df)
#>   consumed produced querySpecies referenceSpecies     pathway_type
#> 1     met5     met4 TFL8958R....     JGE334P,....           shared
#> 2     met1     met5 DOR2356X....     JYF8221A....           shared
#> 3    media     met5                                   unique_query
#> 4     met4     met5                                   unique_query
#> 5     met5     met1                               unique_reference
#> 6     met6     met1                               unique_reference