parse_taxonomy_table

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Parse taxonomic data in a tsv/csv file

Parse taxonomic data in a tsv/csv file

Usage
parse_taxonomy_table(file_path, taxon_col, other_col_type = "obs_info", header = TRUE, sep = "\t", max_lines = NULL, comment_prefix = "#", ...)
Arguments
file_path
(character of length 1) The file path to the input file.
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:
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 0.1.2, License: GPL-2 | GPL-3

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