extract-methods: Method extensions to extraction operator for gbRecord...

In biofiles: An Interface for GenBank/GenPept Flat Files

Description

See the documentation for the Extract generic, defined in the R base-package for the expected behavior.

Usage

## S4 method for signature 'gbFeature,character,missing'
x[[i, j]]

## S4 method for signature 'gbFeature'
x$name

## S4 method for signature 'gbFeatureTable,character,missing'
x[i, j, ..., drop = TRUE]

## S4 method for signature 'gbFeatureTable,numeric,missing'
x[i, j, ..., drop = TRUE]

## S4 method for signature 'gbFeatureTable,logical,missing'
x[i, j, ..., drop = TRUE]

## S4 method for signature 'gbFeatureTable,missing,missing'
x[i, j, ..., drop = TRUE]

## S4 method for signature 'gbFeatureTable,ANY,ANY'
x[[i, j, ...]]

## S4 method for signature 'gbRecord,ANY,missing'
x[i, j, ..., drop = TRUE]

## S4 method for signature 'gbRecord,missing,missing'
x[i, j, ..., drop = TRUE]

## S4 method for signature 'gbRecord,ANY,ANY'
x[[i, j, ...]]

Arguments

x	A gbFeature, gbFeatureTable, or gbRecord object.
i	indices specifying elements to extract. With gbFeatureTables and gbRecords, a character index is matched against feature keys; gbFeatures a character index is matched against qualifiers.
j	Not used.
name	The name of the element to extract.
...	Not used.
drop	Not used.

Value

A gbFeatureTable object or elements of a gbFeature object.

See Also

Extract

Examples

load(system.file("extdata", "marine_metagenome.rda", package = "biofiles"))

## Extract a gbFeatureTable from a gbRecord:
x[1:4]

## Extract a gbFeature
x[[1]]

## Extract ggFeatures by Feature Key
x["CDS"]

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