genbankr (version 1.0.3)

cds,GenBankRecord-method: Annotation extraction api

Description

Accessor functions shared with the larger Bioconductor ecosystem.

Usage

## S3 method for class 'GenBankRecord':
cds(x)
## S3 method for class 'GenBankRecord':
exons(x)
## S3 method for class 'GenBankRecord':
genes(x)
## S3 method for class 'GenBankRecord':
transcripts(x)
## S3 method for class 'GenBankRecord':
getSeq(x, ...)
## S3 method for class 'GenBankFile':
getSeq(x, ...)
## S3 method for class 'GBAccession':
getSeq(x, ...)
## S3 method for class 'GenBankRecord':
cdsBy(x, by = c("tx", "gene"))
## S3 method for class 'GenBankRecord':
exonsBy(x, by = c("tx", "gene"))
## S3 method for class 'GenBankRecord':
isCircular(x)
## S3 method for class '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)