prepare_taxa | R Documentation |
This function performs taxon name preparation to match the Open Tree of Life taxonomy
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
)
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. |
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.
NULL
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