Annotation extraction api

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Description

Accessor functions shared with the larger Bioconductor ecosystem.

Usage

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## 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

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