FROG: Reproducible fitness and robustness diagnostics for constraint-based models

Run a standardized FROG analysis on a model including (1) Objective Function Values, (2) Flux Variability Analysis (FVA), (3) Gene Deletion Fluxes, (4) Reaction Deletion Fluxes.

Usage

frog(model, ...)

# S4 method for class 'ModelOrg'
frog(model, outdir = "frog_report")

# S4 method for class 'character'
frog(model, outdir = "frog_report")

Arguments

model: Model of class ModelOrg or path to SBML file.
...: Additional parameters passed on to the specific method instance.
outdir: Path to output directory, where report files will be saved.

Value

TRUE if frog report export was successful.

References

K. Raman et al., “FROG Analysis Ensures the Reproducibility of Genome Scale Metabolic Models.,” bioRxiv, Sept. 2024. doi: 10.1101/2024.09.24.614797.

Examples

fpath <- system.file("extdata", "e_coli_core.xml", package="cobrar")
mod <- readSBMLmod(fpath)

output_dir <- tempdir()
frog(mod, outdir = output_dir)
#> [1] TRUE

# list files in output directory
dir(output_dir)
#> [1] "01_objective.tsv"                      
#> [2] "02_fva.tsv"                            
#> [3] "03_gene_deletion.tsv"                  
#> [4] "03_reaction_deletion.tsv"              
#> [5] "bslib-b4cb493c4e74a343d7a14e9c9b491bd8"
#> [6] "downlit"                               
#> [7] "e_coli_core.xml"                       
#> [8] "metadata.json"