generate_preprocessed_networks: Generate preprocessed reference databases for MIMOSA2

In borenstein-lab/mimosa2: Model-based Integration of Metabolite Observations and Species Abundances

Generate preprocessed reference databases for MIMOSA2

Description

Generate preprocessed reference databases for MIMOSA2

Usage

generate_preprocessed_networks(
  database,
  model_table_file = NULL,
  picrust_ko_path = "data/picrustGenomeData/",
  kegg_paths = c("data/KEGG/reaction_mapformula.lst", "data/KEGG/reaction_ko.list",
    "data/KEGG/reaction"),
  dat_path = paste0("data/", database, "/"),
  out_path = paste0("data/", database, "/RxnNetworks/")
)

Arguments

database	One of "KEGG", "picrustGG", "AGORA", or "embl_gems"
model_table_file	Optionally, a table listing models from a version of AGORA or embl_gems other than what is included in package data
picrust_ko_path	Path to unzipped precalculated PICRUSt 1 files
kegg_paths	Vector of file paths to the 3 KEGG files required for MIMOSA network template construction (1) reaction_mapformula.lst, 2) reaction_ko.list, and 3) reaction)
dat_path	For the AGORA or embl_gems options, path to directory of .mat model files
out_path	Path to write processed reaction network outputs for each taxon

Value

No return, writes processed reaction network to file

Examples

generate_preprocessed_networks("AGORA", dat_path = "data/AGORA/", )

borenstein-lab/mimosa2 documentation built on Dec. 19, 2024, 12:44 a.m.