Align Consortium Metabolisms

Computes functional alignment between consortium metabolisms. Dispatches on the combination of x and y:

• align(CM, CM): Pairwise alignment of two consortia

• align(CMS): Multiple alignment across all consortia in the set

• align(CM, CMS): Database search – align one consortium against all in a set

Usage

align(x, y, method = "FOS", ...)

# S4 method for class 'ConsortiumMetabolism,ConsortiumMetabolism'
align(x, y, method = "FOS", computePvalue = FALSE, nPermutations = 999L, ...)

# S4 method for class 'ConsortiumMetabolismSet,missing'
align(x, y, method = "FOS", BPPARAM = BiocParallel::SerialParam(), ...)

# S4 method for class 'ConsortiumMetabolism,ConsortiumMetabolismSet'
align(x, y, method = "FOS", BPPARAM = BiocParallel::SerialParam(), ...)

Arguments

x

A ConsortiumMetabolism object (query).

y

A ConsortiumMetabolismSet object (database).

method

Character scalar specifying the metric.

...

Additional arguments (currently unused).

computePvalue

Logical; compute permutation p-value? Default FALSE.

nPermutations

Integer; number of permutations. Default 999L.

BPPARAM

A BiocParallel::BiocParallelParam object. Default BiocParallel::SerialParam().

Value

A ConsortiumMetabolismAlignment object.

A ConsortiumMetabolismAlignment object of type "pairwise".

A ConsortiumMetabolismAlignment object of type "multiple".

A ConsortiumMetabolismAlignment object of type "search".

Functions

• align(x = ConsortiumMetabolism, y = ConsortiumMetabolism): Pairwise alignment of two ConsortiumMetabolism objects

• align(x = ConsortiumMetabolismSet, y = missing): Multiple alignment across all consortia in a ConsortiumMetabolismSet

• align(x = ConsortiumMetabolism, y = ConsortiumMetabolismSet): Database search – align a ConsortiumMetabolism against all consortia in a ConsortiumMetabolismSet

Examples

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: 0.2222
#> Query: "comm_1", Reference: "comm_2"