getDomain: Extractor functions for ConTax data

In microcontax: The ConTax Data Package

Description

Extracting taxonomic information from ConTax data sets.

Usage

getDomain(header)
getPhylum(header)
getClass(header)
getOrder(header)
getFamily(header)
getGenus(header)
getTag(header)
getTaxonomy(header)

Arguments

header

A vector of texts, typically the Header from a table, containing taxonomy information in the proper format.

Details

The ConTax data sets are tables in the FASTA format (see readFasta), where the Header column contains texts according to a strict format.

The header always starts with a short text, a Tag, which is a unique identifier for every sequence. The function getTag will extract this from the header.

After the Tag follows one or more tokens. One of these tokens must be a string with the following format:

"k__<...>;p__<...>;c__<...>;o__<...>;f__<...>;g__<...>;"

where <...> is some proper text. Here is an example of a proper string:

"k__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Staphylococcaceae;g__Staphylococcus;"

The functions getDomain, ..., getGenus extracts the corresponding information from the header. getTaxonomy combines all taxonomy extractors, combines these in a table and imputes missing taxa with parent taxa.

Value

A vector containing the sub-texts extracted from each header text, but getTaxonomy returns a table with the full taxonomy, one row for each input header

Author(s)

Lars Snipen.

See Also

contax.trim, medoids.

Examples

data(contax.trim)
getTag(contax.trim$Header)
getGenus(contax.trim$Header)
getPhylum(contax.trim$Header)

microcontax documentation built on Aug. 11, 2020, 5:08 p.m.