ncbi_byname | R Documentation |
Retrieve gene sequences from NCBI by taxon name and gene names.
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
ncbi_searcher()
, ncbi_byid()
## 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)
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