ncbi_byid {traits} | R Documentation |
Retrieve gene sequences from NCBI by accession number.
Description
Retrieve gene sequences from NCBI by accession number.
Usage
ncbi_byid(ids, format = NULL, verbose = TRUE)
Arguments
ids |
(character) GenBank ids to search for. One or more. Required. |
format |
(character) Return type, e.g., |
verbose |
(logical) If |
Details
If bad ids are included with good ones, the bad ones are silently dropped. If all ids are bad you'll get a stop with error message.
Value
data.frame of the form:
taxon - taxonomic name (may include some junk, but hard to parse off)
taxonomy - organism lineage
gene_desc - gene description
organelle - if mitochondrial or chloroplast
gi_no - GI number
acc_no - accession number
keyword - if official DNA barcode
specimen_voucher - museum/lab accession number of vouchered material
lat_lon - longitude/latitude of specimen collection event
country - country/location of specimen collection event
paper_title - title of study
journal - journal study published in (if published)
first_author - first author of study
uploaded_date - date sequence was uploaded to GenBank
length - sequence length
sequence - sequence character string
Author(s)
Scott Chamberlain, Rupert Collins
See Also
ncbi_searcher()
, ncbi_byname()]
Examples
## Not run:
# A single gene
ncbi_byid(ids="360040093")
# Many genes (with different accession numbers)
ncbi_byid(ids=c("360040093","347448433"))
## End(Not run)