Build a tax_table from a named possibly-jagged list
Build a tax_table from a named possibly-jagged list
build_tax_table(taxlist)
taxlist |
(Required). A list in which each element is a vector of taxonomic assignments named by rank. Every element of every vector must be named by the rank it represents. Every element of the list (every vector) should correspond to a single OTU and be named for that OTU. |
A tax_table (taxonomyTable-class) that
has been built from taxlist. The OTU names of this output will be
the element names of taxlist, and a separate taxonomic rank
(column) will be included for each unique rank found among the element names
of each vector in the list. NA_character_ is the default value of
elements in the tax_table for which there is no corresponding
information in taxlist.
taxvec1 = c("Root", "k__Bacteria", "p__Firmicutes", "c__Bacilli", "o__Bacillales", "f__Staphylococcaceae")
parse_taxonomy_default(taxvec1)
parse_taxonomy_greengenes(taxvec1)
taxvec2 = c("Root;k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Staphylococcaceae")
parse_taxonomy_qiime(taxvec2)
taxlist1 = list(OTU1=parse_taxonomy_greengenes(taxvec1), OTU2=parse_taxonomy_qiime(taxvec2))
taxlist2 = list(OTU1=parse_taxonomy_default(taxvec1), OTU2=parse_taxonomy_qiime(taxvec2))
build_tax_table(taxlist1)
build_tax_table(taxlist2)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.