build_tax_table {phyloseq} | R Documentation

## Build a `tax_table` from a named possibly-jagged list

### Description

Build a `tax_table` from a named possibly-jagged list

### Usage

    build_tax_table(taxlist)

### Arguments

`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.

### Value

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`.

### See Also

`import_biom` `import_qiime`

### Examples

     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)

[Package phyloseq version 1.38.0 Index]