cds,GenBankRecord-method {genbankr} | R Documentation

## 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)

[Package genbankr version 1.22.0 Index]