| read.GenBank {ape} | R Documentation |
This function connects to the GenBank database, and reads nucleotide sequences using accession numbers given as arguments.
read.GenBank(access.nb, seq.names = access.nb,
species.names = TRUE, as.character = FALSE)
access.nb |
a vector of mode character giving the accession numbers. |
seq.names |
the names to give to each sequence; by default the accession numbers are used. |
species.names |
a logical indicating whether to attribute the species names to the returned object. |
as.character |
a logical controlling whether to return the
sequences as an object of class "DNAbin" (the default). |
The function uses the site http://www.ncbi.nlm.nih.gov/ from where the sequences are downloaded.
If species.names = TRUE, the returned list has an attribute
"species" containing the names of the species taken from the
field ``ORGANISM'' in GenBank.
A list of DNA sequences made of vectors of class "DNAbin", or
of single characters (if as.character = "TRUE").
Emmanuel Paradis Emmanuel.Paradis@mpl.ird.fr
read.dna, write.dna,
dist.dna, DNAbin
### This won't work if your computer is not connected
### to the Internet!!!
###
### Get the 8 sequences of tanagers (Ramphocelus)
### as used in Paradis (1997)
ref <- c("U15717", "U15718", "U15719", "U15720",
"U15721", "U15722", "U15723", "U15724")
### Copy/paste or type the following commands if you
### want to try them.
## Not run:
Rampho <- read.GenBank(ref)
### get the species names:
attr(Rampho, "species")
### build a matrix with the species names and the accession numbers:
cbind(attr(Rampho, "species"), names(Rampho))
### print the first sequence
### (can be done with `Rampho$U15717' as well)
Rampho[[1]]
### print the first sequence in a cleaner way
cat(Rampho[[1]], "\n", sep = "")
## End(Not run)