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.