get_taxmap_cols
From metacoder v0.3.3
by Zachary Foster
Get a column subset
Convert logical, names, or indexes to column names and check that they exist.
- Keywords
- internal
Usage
get_taxmap_cols(obj, data, cols = NULL)Arguments
- obj
A taxmap object
- data
The name of a table in
objthat 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
TRUEvalues.- 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"))
# }
Community examples
Looks like there are no examples yet.