pplace_to_taxonomy {BoSSA} | R Documentation |
Convert a pplace object to a taxonomy table
Description
Convert a pplace object to a taxonomy table
Usage
pplace_to_taxonomy(pplace,taxonomy,
rank=c("phylum","class","order","family","genus","species"),
type="all",tax_name=TRUE,run_id=NULL)
Arguments
pplace |
A pplace object |
taxonomy |
The taxonomy table as obtained using the refseq fonction with type set to taxonomy |
rank |
The desired rank for the taxonomy table |
type |
Wether all the possible classification available in the multiclass table are outputed (type="all") or only the best (type="best") |
tax_name |
Wether to use taxonomy names (default) or tax_id number |
run_id |
A vector of run_id to subset |
Value
A matrix with taxonomic ranks for each sequence
Author(s)
pierre lefeuvre
[Package BoSSA version 3.7 Index]