pplace_to_taxonomy {BoSSA}

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