biomartr (version 0.0.1)

read_genome: Read the genome of a given Organism

Description

This function reads an organism specific genome stored in a defined file format.

Usage

read_genome(file, format, ...)

Arguments

file

a character string specifying the path to the file storing the genome.

format

a character string specifying the file format used to store the genome, e.g. "fasta", "gbk".

...

additional arguments that are used by the seqinr::read.fasta() function.

Value

• A data.table storing the gene id in the first column and the corresponding sequence as string in the second column.

Details

The read.genome function takes a string specifying the path to the genome file of interest as first argument.

It is possible to read in different genome file standards such as fasta or genebank. Genomes stored in fasta files can be downloaded from http://ensemblgenomes.org/info/genomes.

Examples

# reading a genome stored in a fasta file
Ath.genome <- read.genome(system.file('seqs/ortho_thal_cds.fasta', package = 'orthologr'),
                           format = "fasta")