biomartr (version 0.5.1)

getProteome: Proteome Retrieval

Description

Main proteome retrieval function for an organism of interest. By specifying the scientific name of an organism of interest the corresponding fasta-file storing the proteome of the organism of interest can be downloaded and stored locally. Proteome files can be retrieved from several databases.

Usage

getProteome(db = "refseq", organism, path = file.path("_ncbi_downloads",
  "proteomes"))

Arguments

db

a character string specifying the database from which the genome shall be retrieved:

• db = "refseq"
• db = "genbank"
• db = "ensembl"
• db = "ensemblgenomes"

organism

a character string specifying the scientific name of the organism of interest, e.g. organism = "Homo sapiens".

path

a character string specifying the location (a folder) in which the corresponding proteome shall be stored. Default is path = file.path("_ncbi_downloads","proteomes").

Value

File path to downloaded proteome.

Details

Internally this function loads the the overview.txt file from NCBI:

refseq: ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/

genbank: ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/

and creates a directory '_ncbi_downloads/proteomes' to store the proteome of interest as fasta file for future processing.

See Also

getGenome, getCDS, getGFF, getRNA, meta.retrieval, read_proteome

Examples

## Not run: ------------------------------------
# 
# # download the proteome of Arabidopsis thaliana from refseq
# # and store the corresponding proteome file in '_ncbi_downloads/proteomes'
# file_path <- getProteome( db       = "refseq", 
#              organism = "Arabidopsis thaliana", 
#              path     = file.path("_ncbi_downloads","proteomes") )
# 
# Ath_proteome <- read_proteome(file_path, format = "fasta")
# 
# # download the proteome of Arabidopsis thaliana from genbank
# # and store the corresponding proteome file in '_ncbi_downloads/proteomes'
# file_path <- getProteome( db       = "genbank", 
#              organism = "Arabidopsis thaliana", 
#              path     = file.path("_ncbi_downloads","proteomes") )
# 
# Ath_proteome <- read_proteome(file_path, format = "fasta")
## ---------------------------------------------