- db
a character string specifying the database from which the genome
shall be retrieved:
db = "refseq"
db = "genbank"
db = "ensembl"
- organism
Organism selector id,
there are three 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 for Homo sapiens
)
by taxonomic identifier from NCBI Taxonomy
: e.g. organism = "9606"
(= taxid of Homo sapiens
)
- reference
a logical value indicating whether or not a genome shall be downloaded if it isn't marked in the database as either a reference genome or a representative genome.
- skip_bacteria
Due to its enormous dataset size (> 700MB as of July 2023),
the bacterial summary file will not be loaded by default anymore. If users
wish to gain insights for the bacterial kingdom they needs to actively specify skip_bacteria = FALSE
. When skip_bacteria = FALSE
is set then the
bacterial summary file will be downloaded.
- release
a numeric, the database release version of ENSEMBL (db = "ensembl"
). Default is release = NULL
meaning
that the most recent database version is used. release = 75
would for human would give the stable
GRCh37 release in ensembl. Value must be > 46, since ensembl did not structure their data
if the standard format before that.
- assembly_type
character, default c("primary_assembly", "toplevel"). Used for ensembl only,
specifies the genome assembly type. Searches for both primary and toplevel, and if both are found, uses the
first by order (so primary is prioritized by default).
The Primary assembly should usually be used if it exists.
The "primary assembly" contains all the top-level sequence regions,
excluding alternative haplotypes and patches.
If the primary assembly file is not present for a species
(only defined for standard model organisms),
that indicates that there were no haplotype/patch regions,
and in such cases, the 'toplevel file is used.
For more details see:
ensembl tutorial
- analyse_genome
logical, default FALSE. If TRUE, get general genome statistics like
gc content etc. For more details, see ?summary_genome
- remove_annotation_outliers
shall outlier lines be removed from the input annotation_file
?
If yes, then the initial annotation_file
will be overwritten and the removed outlier lines will be stored at tempdir
for further exploration.
- gunzip
a logical, indicating whether or not files should be unzipped.
- path
a character string specifying the location (a folder) in which
the corresponding collection shall be stored. Default is
path
= file.path("_db_downloads","collections")
.
- mute_citation
logical, default FALSE, indicating whether citation message should be muted.