ncbi_byname
From traits v0.1.0
by Scott Chamberlain
Retrieve gene sequences from NCBI by taxon name and gene names.
Retrieve gene sequences from NCBI by taxon name and gene names.
Usage
ncbi_byname(taxa, gene = "COI", seqrange = "1:3000", getrelated = FALSE,
verbose = TRUE)
Arguments
- 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.,
"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. IfFALSE
, returns nothing if no match found. - verbose
- (logical) If
TRUE
(default), informative messages printed.
Details
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.
Value
- Data.frame of results.
See Also
Examples
# A single species
ncbi_byname(taxa="Acipenser brevirostrum")
# Many species
species <- c("Colletes similis","Halictus ligatus","Perdita trisignata")
ncbi_byname(taxa=species, gene = c("coi", "co1"), seqrange = "1:2000")
Community examples
Looks like there are no examples yet.