| read.GB {spider} | R Documentation |
Download sequences from Genbank with metadata.
Description
Downloads sequences associated with the given accession numbers into a ‘DNAbin’ class.
Usage
read.GB(access.nb, seq.names = access.nb, species.names = TRUE,
gene = TRUE, access = TRUE, as.character = FALSE)
Arguments
access.nb |
A character vector giving the GenBank accession numbers to download. |
seq.names |
A character vector giving the names to give to each sequence. Defaults to "accession number | species name". |
species.names |
Logical. Should species names be downloaded? Default of TRUE. |
gene |
Logical. Should the name of the gene region be downloaded? Default of TRUE. |
access |
Logical. Should the accession number be downloaded? Default of TRUE. |
as.character |
Logical. Should the sequences be returned as character vector? Default of FALSE, function returns sequences as a ‘DNAbin’ object. |
Details
This function is a modification of
read.GenBank to include metadata with each
sequence. Additional data currently implemented are the species names and
the gene region from which sequences were derived.
Value
A 'DNAbin' object with the following attributes: "species",
"gene", and "accession_num".
Warning
15 Feb 2018: 'read.GB' is deprecated. Please use the rOpenSci packages 'rentrez' and 'traits', or 'ape' for better functionality.
Author(s)
Samuel Brown <s_d_j_brown@hotmail.com>
See Also
Examples
## Not run:
read.GB("AY059961")
#Download the sequences making data(anoteropsis) from Genbank
nums <- 59961:59993
seqs <- paste("AY0", nums, sep="")
dat <- read.GB(seqs)
attr(dat, "species")
attr(dat, "gene")
attr(dat, "accession_num")
## End(Not run)