read.seqgen {phyclust} | R Documentation |
Read seqgen's Results and Return a seq.data
Description
This function can read the results generated by seqgen
and
turn into a object in Class seq.data
.
Usage
read.seqgen(text, byrow = TRUE, code.type = .code.type[1])
Arguments
text |
a text vector generated by |
byrow |
advanced option, default = TRUE. |
code.type |
either "NUCLEOTIDE" (default) or "SNP". |
Details
If code.type
is "SNP", the A, G will be transfered to 1, and
the C, T will be transfered to 2.
Value
Return an object in Class seq.data
.
Author(s)
Wei-Chen Chen wccsnow@gmail.com
References
Phylogenetic Clustering Website: https://snoweye.github.io/phyclust/
See Also
seqgen
,
gen.seq.HKY
,
gen.seq.SNP
.
Examples
## Not run:
library(phyclust, quiet = TRUE)
set.seed(123)
ret.ms <- ms(nsam = 5, nreps = 1, opts = "-T")
ret.seqgen <- seqgen(opts = "-mHKY -l40 -s0.2", newick.tree = ret.ms[3])
(ret.nucleotide <- read.seqgen(ret.seqgen))
(ret.snp <- read.seqgen(ret.seqgen, code.type = "SNP"))
## End(Not run)
[Package phyclust version 0.1-34 Index]