Main GFF retrieval function for a set of organism of interest. By specifying the scientific names of the organisms of interest the corresponding fasta-files storing the GFF of the organisms of interest will be downloaded and stored locally. GFF files can be retrieved from several databases.
Usage
getGFFSet(
db = "refseq",
organisms,
reference = FALSE,
release = NULL,
clean_retrieval = TRUE,
gunzip = TRUE,
remove_annotation_outliers = FALSE,
update = FALSE,
path = "set_GFF"
)
Arguments
- db
a character string specifying the database from which the GFF shall be retrieved:
db = "refseq"
db = "genbank"
db = "ensembl"
- organisms
a character vector storing the names of the organisms than shall be retrieved. There are three available options to characterize an organism:
by
scientific name
: e.g.organism = "Homo sapiens"
by
database specific accession identifier
: e.g.organism = "GCF_000001405.37"
(= NCBI RefSeq identifier forHomo sapiens
)by
taxonomic identifier from NCBI Taxonomy
: e.g.organism = "9606"
(= taxid ofHomo sapiens
)
- reference
a logical value indicating whether or not a GFF shall be downloaded if it isn't marked in the database as either a reference GFF or a representative GFF
- release
the database release version of ENSEMBL (
db = "ensembl"
). Default isrelease = NULL
meaning that the most recent database version is used.- clean_retrieval
logical value indicating whether or not downloaded files shall be renamed for more convenient downstream data analysis.
- gunzip
a logical value indicating whether or not files should be unzipped.
- remove_annotation_outliers
shall outlier lines be removed from the input
annotation_file
? If yes, then the initialannotation_file
will be overwritten and the removed outlier lines will be stored attempdir
for further exploration.- update
a logical value indicating whether or not files that were already downloaded and are still present in the output folder shall be updated and re-loaded (
update = TRUE
or whether the existing file shall be retainedupdate = FALSE
(Default)).- path
a character string specifying the location (a folder) in which the corresponding CDSs shall be stored. Default is
path
="set_CDS"
.
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 'set_CDSs' to store the CDSs of interest as fasta files for future processing. In case the corresponding fasta file already exists within the 'set_CDSs' folder and is accessible within the workspace, no download process will be performed.
Examples
if (FALSE) {
getGFFSet("refseq", organisms = c("Arabidopsis thaliana",
"Arabidopsis lyrata",
"Capsella rubella"))
}