Import Proteome as Biostrings or data.table object

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

Usage

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

Arguments

file

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

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 read.fasta.

Value

Either a Biostrings or data.table object.

Details

This function takes a string specifying the path to the proteome file of interest as first argument.

It is possible to read in different proteome file standards such as fasta or genebank.

See also

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

Other proteome: getProteomeSet(), getProteome()

Author

Hajk-Georg Drost