download_reference_data: Uses the provided OTU table to generate a contribution table...

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

Uses the provided OTU table to generate a contribution table based on the PICRUSt 16S normalization and genomic content tables

Description

Uses the provided OTU table to generate a contribution table based on the PICRUSt 16S normalization and genomic content tables

Usage

download_reference_data(
  seq_db = get_text("database_choices")[1],
  target_db = get_text("source_choices")[2],
  save_to = paste0(getwd(), "/"),
  source_url = "http://elbo-spice.cs.tau.ac.il/shiny/MIMOSA2shiny/refData/"
)

Arguments

seq_db	Microbiome data source type: must be one of "Sequence variants (ASVs)", "Greengenes 13_5 or 13_8 OTUs", or "SILVA 132 OTUs"
target_db	Metabolic network source: must be one of "AGORA genomes and models" or "RefSeq/EMBL_GEMs genomes and models" (for KEGG models, see documentation)
save_to	File path to save the downloaded data. Default is a folder named "data/" in the current working directory

Value

None

Examples

download_reference_data("Sequence variants (ASVs)", "AGORA genomes and models")

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