get_taxmap_cols: Get a column subset

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

Get a column subset

Description

Convert logical, names, or indexes to column names and check that they exist.

Usage

get_taxmap_cols(obj, data, cols = NULL)

Arguments

obj	A taxmap object
data	The name of a table in obj that contains counts.
cols	The columns in the data set to use. 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_data(), get_taxmap_other_cols(), get_taxmap_table(), verify_taxmap()

Examples

## Not run: 
# Parse data
x = parse_tax_data(hmp_otus, class_cols = "lineage", class_sep = ";",
                   class_key = c(tax_rank = "taxon_rank", tax_name = "taxon_name"),
                   class_regex = "^(.+)__(.+)$")
                   
# Get all col names
metacoder:::parse_taxmap_cols(x, "tax_data")

# Get col names by index
metacoder:::parse_taxmap_cols(x, "tax_data", 2:4)

# Get col names by name (i.e. verify)
metacoder:::parse_taxmap_cols(x, "tax_data", c("taxon_id", "lineage"))
metacoder:::parse_taxmap_cols(x, "tax_data", c("taxon_id", "not_valid"))

# Get colnames by TRUE/FALSE vector
metacoder:::parse_taxmap_cols(x, "tax_data", startsWith(colnames(x$data$tax_data), "7"))
                   

## End(Not run)

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