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Retrieve Metabolic Pathways

Source: R/AllGenerics.R, R/methods-pathways.R
pathways.Rd

Retrieves the pathways representing metabolic interactions between species.

By default, returns a concise summary with columns consumed, produced, and n_species. For ConsortiumMetabolismSet objects, n_cons is included as well. Set verbose = TRUE to return the full pathway data including flux statistics, indices, and per-species detail.

The argument type can be used to return only specific types of pathways from a ConsortiumMetabolismSet object:

  • "all" returns all pathways

  • "pan-cons" returns pathways present in most consortia

  • "niche" returns niche pathways specific to few consortia

  • "core" returns core metabolic pathways shared across most species

  • "aux" returns auxiliary pathways found in few species

Usage

pathways(object, ...)

# S4 method for class 'ConsortiumMetabolism'
pathways(object, verbose = FALSE)

# S4 method for class 'ConsortiumMetabolismSet'
pathways(
  object,
  type = c("all", "pan-cons", "niche", "core", "aux"),
  quantileCutoff = 0.1,
  verbose = FALSE
)

# S4 method for class 'ConsortiumMetabolismAlignment'
pathways(object)

Arguments

object

A ConsortiumMetabolism, ConsortiumMetabolismSet, or ConsortiumMetabolismAlignment object.

...

Object specific arguments. See methods for details.

verbose

Logical scalar. If FALSE (default), returns a concise summary with columns consumed, produced, and n_species. If TRUE, returns the full pathway data including flux statistics, effective values, and per-species detail.

type

Character scalar giving the type of pathways to output.

quantileCutoff

Numeric scalar between 0 and 1 giving the quantile threshold to use for filtering pathways. For "pan-cons" and "core" types, pathways above 1 - quantileCutoff are returned. For "niche" and "aux" types, pathways below quantileCutoff are returned. Defaults to 0.1 (i.e., top/bottom 10 percent).

Value

A data.frame of pathway information. With verbose = FALSE (default): consumed, produced, n_species (and n_cons for CMS objects). With verbose = TRUE: all available columns including flux statistics and indices.

Methods (by class)

  • pathways(ConsortiumMetabolism): Get Pathways From a ConsortiumMetabolism Object

  • pathways(ConsortiumMetabolismSet): Get Pathways From a ConsortiumMetabolismSet Object

  • pathways(ConsortiumMetabolismAlignment): Get Pathways From a ConsortiumMetabolismAlignment Object

Examples

cm <- synCM("test", n_species = 3, max_met = 5)
pathways(cm)
#> # A tibble: 5 × 3
#>   consumed produced n_species
#>   <chr>    <chr>        <dbl>
#> 1 met5     met2             2
#> 2 met4     met3             1
#> 3 met5     met3             1
#> 4 met2     met3             1
#> 5 met4     met2             1
pathways(cm, verbose = TRUE)
#> # A tibble: 5 × 12
#>   consumed produced data     n_species  c_sum p_sum c_prob    p_prob c_eff p_eff
#>   <chr>    <chr>    <list>       <dbl>  <dbl> <dbl> <list>    <list> <dbl> <dbl>
#> 1 met5     met2     <tibble>         2 11.8    5.01 <dbl [2]> <dbl>   1.92  1.86
#> 2 met4     met3     <tibble>         1  0.762  1.76 <dbl [1]> <dbl>   1     1   
#> 3 met5     met3     <tibble>         1  1.09   1.76 <dbl [1]> <dbl>   1     1   
#> 4 met2     met3     <tibble>         1  5.25   1.76 <dbl [1]> <dbl>   1     1   
#> 5 met4     met2     <tibble>         1  4.65   3.45 <dbl [1]> <dbl>   1     1   
#> # ℹ 2 more variables: c_ind <int>, p_ind <int>