Prepare taxa — prepare

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$raw,
  extension = get_params(step = "prepare_taxa")$names$extension,
  name_features = get_params(step = "prepare_taxa")$names$features,
  name_filename = get_params(step = "prepare_taxa")$names$filename,
  colname = get_params(step = "prepare_taxa")$names$taxon,
  metadata = get_params(step = "prepare_taxa")$files$metadata$raw,
  top_k = get_params(step = "prepare_taxa")$organisms$candidates,
  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_features: Name of the features column in the features file
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
top_k: Number of organisms to be retained per feature top intensities
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.

Value

The path to the prepared taxa

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.

Examples

if (FALSE) { # \dontrun{
tima:::copy_backbone()
go_to_cache()
github <- "https://raw.githubusercontent.com/"
repo <- "taxonomicallyinformedannotation/tima-example-files/main/"
dir <- paste0(github, repo)
org_tax_ott <- get_params(step = "prepare_taxa")$files$libraries$sop$merged$organisms$taxonomies$ott |>
  gsub(
    pattern = ".gz",
    replacement = "",
    fixed = TRUE
  )
get_file(url = paste0(dir, org_tax_ott), export = org_tax_ott)
get_file(
  url = get_default_paths()$urls$examples$features,
  export = get_params(step = "prepare_taxa")$files$features$raw
)
prepare_taxa(
  taxon = "Homo sapiens",
  org_tax_ott = org_tax_ott
)
unlink("data", recursive = TRUE)
} # }