GenbankGenome: R6 Class for loading and analysing Genbank whole genome files

In sagrudd/floundeR: Toolkit For Nanopore Sequence Analysis

R6 Class for loading and analysing Genbank whole genome files

Description

This class aims to implement a couple of trivial methods for wrangling whole microbial genome information from Genbank files

Super class

floundeR::FloundeR -> GenbankGenome

Methods

Public methods

• GenbankGenome$new()

• GenbankGenome$list_cds()

• GenbankGenome$get_cds()

• GenbankGenome$focus_cds()

• GenbankGenome$focus_range()

• GenbankGenome$as_tibble()

• GenbankGenome$whole_genome_focus()

• GenbankGenome$focus_nucleotide()

• GenbankGenome$focus_codon()

• GenbankGenome$get_nucleotide()

• GenbankGenome$unfocus()

• GenbankGenome$is_focused()

• GenbankGenome$get_focus()

• GenbankGenome$clone()

Inherited methods

• floundeR::FloundeR$bin_data()
• floundeR::FloundeR$num_scale()
• floundeR::FloundeR$nums_scale()
• floundeR::FloundeR$print()

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Method new()

Creates a new GenbankGenome object. This initialisation method performs minimal sanity checking of the defined file(s)

Usage

GenbankGenome$new(gb_file)

Arguments

gb_file

The source sequencing_summary file.

Returns

A new GenbankGenome object.

Examples

TB_reference = flnDr("TB_H37Rv.gb.gz")
tb <- GenbankGenome$new(TB_reference)

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Method list_cds()

exports the annotated genomic features as a GenomicRanges object. This can be used for the review of content in a genomics context.

Usage

GenbankGenome$list_cds()

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Method get_cds()

Get the CDS information for one or more annotated features from the genome of interest.

Usage

GenbankGenome$get_cds(feature_id = "fusA1")

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Method focus_cds()

Usage

GenbankGenome$focus_cds(feature_id = "fusA1")

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Method focus_range()

Usage

GenbankGenome$focus_range(chromosome = NULL, start = NULL, end = NULL)

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Method as_tibble()

Usage

GenbankGenome$as_tibble()

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Method whole_genome_focus()

Usage

GenbankGenome$whole_genome_focus()

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Method focus_nucleotide()

Usage

GenbankGenome$focus_nucleotide(position)

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Method focus_codon()

Usage

GenbankGenome$focus_codon(codon)

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Method get_nucleotide()

Usage

GenbankGenome$get_nucleotide(position, strand)

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Method unfocus()

Usage

GenbankGenome$unfocus()

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Method is_focused()

Usage

GenbankGenome$is_focused()

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Method get_focus()

Usage

GenbankGenome$get_focus()

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Method clone()

The objects of this class are cloneable with this method.

Usage

GenbankGenome$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

## ------------------------------------------------
## Method `GenbankGenome$new`
## ------------------------------------------------

TB_reference = flnDr("TB_H37Rv.gb.gz")
tb <- GenbankGenome$new(TB_reference)

sagrudd/floundeR documentation built on Nov. 18, 2022, 10:31 a.m.