Import Genome Assembly as Biostrings or data.table object

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

Usage

read_genome(file, format = "fasta", obj.type = "Biostrings", ...)

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. format = "fasta" (default) or format = "gbk".

obj.type

a character string specifying the object stype in which the genomic sequence shall be represented. Either as obj.type = "Biostrings" (default) or as obj.type = "data.table".

...

additional arguments that are used by the read.fasta function.

Value

Either a Biostrings or data.table object.

Details

This function takes a string specifying the path to the genome file of interest as first argument (e.g. the path returned by getGenome).

See also

Other genome: getGenome(), getGenomeSet()

Other readers: read_cds(), read_gff(), read_proteome(), read_rna()

Author

Hajk-Georg Drost