getGTF: Genome Annotation Retrieval (GTF)

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/getGTF.R

Description

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

Usage

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getGTF(db = "ensembl", organism, path = file.path("ensembl", "annotation"))

Arguments

db

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

  • 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 annotation file shall be stored. Default is path = file.path("ensembl","annotation").

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 'ensembl/annotation' to store the genome of interest as fasta file for future processing. In case the corresponding fasta file already exists within the 'ensembl/annotation' folder and is accessible within the workspace, no download process will be performed.

Value

File path to downloaded annotation file.

Author(s)

Hajk-Georg Drost

See Also

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

Examples

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## Not run: 
# download the annotation of Arabidopsis thaliana from refseq
# and store the corresponding genome file in 'ensembl/annotation'
getGTF( db       = "ensembl", 
               organism = "Homo sapiens", 
               path = file.path("ensembl","annotation"))


## End(Not run)

biomartr documentation built on July 2, 2018, 1:02 a.m.