Description Usage Arguments Details Value Author(s) See Also Examples
Retrieve gene sequences from NCBI by taxon name and gene names.
1 2 3 4 5 6 7 8 | ncbi_byname(
taxa,
gene = "COI",
seqrange = "1:3000",
getrelated = FALSE,
verbose = TRUE,
...
)
|
taxa |
(character) Scientific name to search for. |
gene |
(character) Gene or genes (in a vector) to search for. See examples. |
seqrange |
(character) Sequence range, as e.g., |
getrelated |
(logical) If |
verbose |
(logical) If |
... |
Curl options passed on to crul::verb-GET |
Removes predicted sequences so you don't have to remove them. Predicted sequences are those with accession numbers that have "XM_" or "XR_" prefixes. This function retrieves one sequences for each species, picking the longest available for the given gene.
data.frame
Scott Chamberlain
1 2 3 4 5 6 7 8 9 | ## Not run:
# A single species
ncbi_byname(taxa="Acipenser brevirostrum")
# Many species
species <- c("Colletes similis","Halictus ligatus","Perdita californica")
ncbi_byname(taxa=species, gene = c("coi", "co1"), seqrange = "1:2000")
## End(Not run)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.