parse_taxonomy_table

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Percentile

Parse taxonomic data in a tsv/csv file

Parse taxonomic data in a tsv/csv file

Usage
parse_taxonomy_table(input, taxon_col, other_col_type = "obs_info",
  header = TRUE, sep = "\t", max_lines = NULL, comment_prefix = "#",
  ...)
Arguments
input

(character of length 1) The file path to the input file or a data.frame.

taxon_col

(named integer of length 1) The index of the column with taxonomic information, named by the type of information. A negative index is interpreted as the number of columns from the last. The name of the column can have to following values:

taxon_id

A unique numeric id for a taxon for a particular database (e.g. ncbi accession number). Requires an internet connection.

name

The name of a taxon. Not necessarily unique, but are interpretable by a particular database. Requires an internet connection.

class

A list of taxa information that constitutes the full taxonomic classification from broad to specific (see class_rev) for a particular database. Individual taxa are separated by the class_sep argument and the information is parsed by the class_regex and class_key arguments.

other_col_type

(character) The type of the other columns no specified by taxon_col. Can be "taxon_info" or "obs_info".

header

(logical of length 1) If TRUE, the first row of the file is the column names.

sep

(character of length 1) The character(s) that separate each column in each row. Can be a regular expression.

max_lines

(integer of length 1) The maximum number of lines to read from the file.

comment_prefix

(character) One or more characters that appear at the start of a line indicating that the line is a comment and not part of the data.

...

Passed to extract_taxonomy.

Value

taxmap

Aliases
  • parse_taxonomy_table
Documentation reproduced from package metacoder, version 0.1.3, License: GPL-2 | GPL-3

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