Prepare taxa

Description

This function performs taxon name preparation to match the Open Tree of Life taxonomy

Usage

prepare_taxa(
  input = get_params(step = "prepare_taxa")\$files\$features\$prepared,
  extension = get_params(step = "prepare_taxa")\$names\$extension,
  name_filename = get_params(step = "prepare_taxa")\$names\$filename,
  colname = get_params(step = "prepare_taxa")\$names\$taxon,
  metadata = get_params(step = "prepare_taxa")\$files\$metadata\$raw,
  org_tax_ott = get_params(step =
    "prepare_taxa")\$files\$libraries\$sop\$merged\$organisms\$taxonomies\$ott,
  output = get_params(step = "prepare_taxa")\$files\$metadata\$prepared,
  taxon = get_params(step = "prepare_taxa")\$organisms\$taxon
)

Arguments

input File containing your features intensities
extension Does your column names contain the file extension? (mzmine mainly)
name_filename Name of the file name column in the metadata file
colname Name of the column containing biological source information
metadata File containing your metadata including biological source
org_tax_ott File containing Open Tree of Life Taxonomy
output Output file
taxon If you want to enforce all features to a given taxon, put its name here.

Details

Depending if the features are aligned between samples originating from various organisms or not, It can either attribute all features to a single organism, or attribute them to multiple ones, according to their relative intensities among the samples.

Value

The path to the prepared taxa

Examples

library("tima")

copy_backbone()
go_to_cache()
github <- "https://raw.githubusercontent.com/"
repo <- "taxonomicallyinformedannotation/tima-example-files/main/"
dir <- paste0(github, repo)
org_tax_ott <- paste0(
  "data/interim/libraries/",
  "sop/merged/organisms/taxonomies/ott.tsv"
)
get_file(url = paste0(dir, org_tax_ott), export = org_tax_ott)
get_file(
  url = paste0(dir, "data/interim/features/example_features.tsv"),
  export = get_params(step = "prepare_taxa")$files$features$prepared
)
prepare_taxa(
  taxon = "Homo sapiens",
  org_tax_ott = org_tax_ott
)
unlink("data", recursive = TRUE)