api-methods: Annotation extraction api

In gmbecker/genbankr: Parsing GenBank files into semantically useful objects

Annotation extraction api

Description

Accessor functions shared with the larger Bioconductor ecosystem.

Usage

## S4 method for signature 'GenBankRecord'
cds(x)

## S4 method for signature 'GenBankRecord'
exons(x)

## S4 method for signature 'GenBankRecord'
genes(x)

## S4 method for signature 'GenBankRecord'
transcripts(x)

## S4 method for signature 'GenBankRecord'
getSeq(x, ...)

## S4 method for signature 'GenBankFile'
getSeq(x, ...)

## S4 method for signature 'GBAccession'
getSeq(x, ...)

## S4 method for signature 'GenBankRecord'
cdsBy(x, by = c("tx", "gene"))

## S4 method for signature 'GenBankRecord'
exonsBy(x, by = c("tx", "gene"))

## S4 method for signature 'GenBankRecord'
isCircular(x)

## S4 method for signature 'GenBankRecord'
seqinfo(x)

Arguments

x	The object containing the annotations
...	unused.
by	character. Factor to group the resulting GRanges by.

Value

The expected types, GenomicRanges for most functions, a DNAStrimgSet for getSeq

Examples

gb = readGenBank(system.file("sample.gbk", package="genbankr"))
cds(gb)
exons(gb)
genes(gb)

gmbecker/genbankr documentation built on Oct. 30, 2023, 9:24 a.m.