import_mothur_constaxonomy {phyloseq} | R Documentation

## Import mothur constaxonomy file and return a taxonomyTable

### Description

Import mothur constaxonomy file and return a taxonomyTable

### Usage

    import_mothur_constaxonomy(mothur_constaxonomy_file,
      parseFunction = parse_taxonomy_default)

### Arguments

`mothur_constaxonomy_file` | (Required). A consensus taxonomy file produced by mothur.
`parseFunction` | (Optional). A specific function used for parsing the taxonomy string. See `parse_taxonomy_default` for an example. If the default is used, this function expects a semi-colon delimited taxonomy string, with no additional rank specifier. A common taxonomic database is GreenGenes, and for recent versions its taxonomy includes a prefix, which is best cleaved and used to precisely label the ranks (`parse_taxonomy_greengenes`).

### Value

An `taxonomyTable-class` object.

### See Also

`import_mothur`

`tax_table`

`phyloseq`

[Package phyloseq version 1.28.0 Index]