View source: R/consensus.pyRAD.R
consensus.pyRAD | R Documentation |
Uses consensusString
[S4 method for signature 'DNAStringSet']
from the Biostrings
package to create
a consensus sequence for each locus in a pyRAD.loci
object. All options
in consensusString
can be passed in. As a side-effect, writes
a fasta-style file to writeFile
.
consensus.pyRAD(pyIn, from = NA, to = NA, fastaNames = T,
writeFile = 'rads.con.txt', cores = 1, ...)
pyIn |
an object of class |
from |
first locus to summarize (by number, sequentially from the beginning of the file),
or |
to |
last locus to summarize (by number, sequentially from the beginning of the file),
or |
fastaNames |
use |
writeFile |
filename to which to write the sequences |
cores |
number of cores to use; requires the |
... |
extra arguments to |
A character vector of sequences, with locus names as the vector names.
Andrew Hipp
data(oak.rads)
# provide filename for export in line below
temp = consensus.pyRAD(oak.rads, from=1, to = 10, writeFile = NA)
temp
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