qualif-methods: Get/set qualifiers of GenBank features

In biofiles: An Interface for GenBank/GenPept Flat Files

Description

Get/set qualifiers of GenBank features

Usage

qualif(x, which = "", ...)

qualif(x, which, check = TRUE) <- value

## S4 method for signature 'gbFeature'
qualif(x, which, fixed = FALSE, use.names = TRUE)

## S4 replacement method for signature 'gbFeature'
qualif(x, which, check = TRUE) <- value

## S4 method for signature 'gbFeatureTable'
qualif(x, which = "", fixed = FALSE,
  use.names = TRUE)

## S4 method for signature '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

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"])

biofiles documentation built on May 2, 2019, 3:31 p.m.