read_proteome {biomartr}

Import Proteome as Biostrings or data.table object

Description

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.

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.

Value

Either a Biostrings or data.table object.

Author(s)

Hajk-Georg Drost

See Also

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

Other proteome: getProteomeSet(), getProteome()