Usage
ncbi_search(taxa = NULL, id = NULL, seqrange = "1:3000",
getrelated = FALSE, limit = 500, entrez_query = NULL,
hypothetical = FALSE, verbose = TRUE)
Arguments
taxa
(character) Scientific name to search for.
id
(character) Taxonomic id to search for. Not compatible with argument taxa.
seqrange
(character) Sequence range, as e.g., "1:1000". This is the range of
sequence lengths to search for. So "1:1000" means search for sequences from 1 to 1000
characters in length.
getrelated
(logical) If TRUE, gets the longest sequences of a species
in the same genus as the one searched for. If FALSE, returns nothing if no match
found.
limit
(numeric) Number of sequences to search for and return. Max of 10,000.
If you search for 6000 records, and only 5000 are found, you will of course
only get 5000 back.
entrez_query
(character; length 1) An Entrez-format query to filter results with.
This is useful to search for sequences with specific characteristics. The format is the same
as the one used to seach genbank.
(http://www.ncbi.nlm.nih.gov/books/NBK383
hypothetical
(logical; length 1) If FALSE, an attempt will be made to not
return hypothetical or predicted sequences judging from accession number prefixs (XM and XR).
This can result in less than the limit being returned even if
verbose
(logical) If TRUE (default), informative messages printed.