biofiles (version 1.0.0)

qualif: Get/set qualifiers of GenBank features

Description

Get/set qualifiers of GenBank features

Usage

qualif(x, which = "", ...)
qualif(x, which, check = TRUE) <- value
# S4 method for gbFeature
qualif(x, which, fixed = FALSE, use.names = TRUE)
# S4 method for gbFeature
qualif(x, which, check = TRUE) <- value
# S4 method for gbFeatureTable
qualif(x, which = "", fixed = FALSE,
  use.names = TRUE)
# S4 method for gbRecord
qualif(x, which = "", fixed = FALSE,
  use.names = TRUE)

Arguments

x

A '>gbFeature, '>gbFeatureTable, or '>gbRecord object.

which

A character vector giving the name(s) of the qualifiers to retrieve or set.

...

Additional arguments passed to methods.

check

if FALSE, don't perform validity checks.

value

The qualifier information to set on x.

fixed

If TRUE, which is matched against qualifiers as is, if FALSE it is treated as a regular expression.

use.names

If TRUE, return a data.frame using which as column names, if FALSE return, if possible, a character vector or a list.

Value

A data.frame.

Examples

# NOT RUN {
load(system.file("extdata", "marine_metagenome.rda", package = "biofiles"))
qualif(x[[1]], 'db_xref')

## use shortcuts to common qualifiers
proteinID(x["CDS"])
locusTag(x["CDS"])
# }