biomartr (version 0.0.1)

read_proteome: Read the proteome of a given Organism

Description

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

Usage

read_proteome(file, format, ...)

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 proteome, 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.proteome 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.

Proteomes stored in fasta files can be downloaded from http://www.ebi.ac.uk/reference_proteomes.

Examples

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