get_taxmap_other_cols: Parse the other_cols option

In metacoder: Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data

Parse the other_cols option

Description

Parse the other_cols option used in many calculation functions.

Usage

get_taxmap_other_cols(obj, data, cols, other_cols = NULL)

Arguments

obj	A taxmap object
data	The name of a table in obj that contains counts.
cols	The names/indexes of columns in data to use. Takes one of the following inputs: TRUE/FALSE: All columns will used. Vector of TRUE/FALSE of length equal to the number of columns: Use the columns corresponding to TRUE values. Character vector: The names of columns to use Numeric vector: The indexes of columns to use
other_cols	Preserve in the output non-target columns present in the input data. The "taxon_id" column will always be preserved. Takes one of the following inputs: TRUE/FALSE: All non-target columns will be preserved or not. Vector of TRUE/FALSE of length equal to the number of columns: Preserve the columns corresponding to TRUE values. Character vector: The names of columns to preserve Numeric vector: The indexes of columns to preserve

See Also

Other option parsers: get_taxmap_cols(), get_taxmap_data(), get_taxmap_table(), verify_taxmap()

Examples

## Not run: 
# Parse data for examples
x = parse_tax_data(hmp_otus, class_cols = "lineage", class_sep = ";",
                   class_key = c(tax_rank = "taxon_rank", tax_name = "taxon_name"),
                   class_regex = "^(.+)__(.+)$")

# If all cols are used, there are no other cols, only "taxon_id"
metacoder:::get_taxmap_other_cols(x, data = "tax_data", cols = TRUE)

# If a subset of target columns is specified, the rest are returned 
metacoder:::get_taxmap_other_cols(x, data = "tax_data", cols = 2:3)

# Additionally, a subset of other columns can be specified
metacoder:::get_taxmap_other_cols(x, data = "tax_data", cols = 2:3,
                                  other_cols = 4:5)
                   

## End(Not run)

metacoder documentation built on April 4, 2023, 9:08 a.m.