ranges: Extract features as '"GRanges"' objects.

In gschofl/biofiles: An Interface for GenBank/GenPept Flat Files

Description

Extract features as "GRanges" objects.

Usage

ranges(x, join = FALSE, key = TRUE, include = "none", exclude = "", ...)

## S4 method for signature 'gbFeature'
ranges(x, join = FALSE, key = TRUE, include = "none", exclude = "", ...)

## S4 method for signature 'gbFeatureTable'
ranges(x, join = FALSE, key = TRUE, include = "none", exclude = "", ...)

## S4 method for signature 'gbRecord'
ranges(x, join = FALSE, key = TRUE, include = "none", exclude = "", ...)

## S4 method for signature 'gbRecordList'
ranges(x, join = FALSE, key = TRUE, include = "none", exclude = "", ...)

Arguments

x	A gbFeature, gbFeatureTable, gbRecord, or gbRecordList object.
join	Join compound genomic locations into a single range.
key	Include feature keys with ranges.
include	Include qualifiers as metadata columns. Can be "none", "all", or a character vector of qualifier tags.
exclude	Exclude specific qualifiers.
...	Further arguments passed to methods.

Value

A GRanges or GRangesList object.

See Also

start, end, span, strand, location, key, qualif

Examples

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

## default "GRanges" object.
ranges(x)

## subset CDSs and include "product", "note", "protein_id" as metadata.
ranges(x["CDS"], include = c("product", "note", "protein_id"))

## subset CDSs and exclude "translation"
ranges(x["CDS"], include = "all", exclude = "translation")

gschofl/biofiles documentation built on Sept. 27, 2020, 12:08 a.m.