The lineage information is provided in form of a matrix, which contains for each OTU identifier the taxonomic levels from column 2 to 8 (domain, phylum, class, order, family, genus, species) and the entire lineage in column 9. The lineage in column 9 is optional. Alternatively, OTU identifiers can also be stored as column names. In this case, taxonomic levels are assumed to range from column 1 to 7. To differentiate between these two formats, set useRownames to false or true.
getTaxonomy(selected = c(), lineages, level = "class", useRownames = FALSE)
| selected | a character vector of selected OTU identifiers |
|---|---|
| lineages | a lineage table |
| level | the taxonomic level (domain, phylum, class, order, family, genus or species) |
| useRownames | match OTU identifiers to row names instead of the first column (in this case, taxonomic levels are assumed to range from column 1 to 7) |
the taxonomy of the OTUs
data(david_stoolA_otus) data(david_stool_lineages) sorted=sort(apply(david_stoolA_otus,1,sum),decreasing=TRUE)[1:10] getTaxonomy(names(sorted),david_stool_lineages,level="family")#> [1] Ruminococcaceae Bacteroidaceae Erysipelotrichaceae #> [4] Bacteroidaceae Ruminococcaceae none #> [7] Lachnospiraceae Bifidobacteriaceae Lachnospiraceae #> [10] Lachnospiraceae #> 152 Levels: A29 ACK-M1 AKIW874 Acetobacteraceae ... none