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.
Examples
if (FALSE) { # \dontrun{
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)
} # }