| gen.seq {phyclust} | R Documentation |
These functions call seqgen to generate sequences by
evolutions models based on a rooted tree. gen.seq.HKY is to
generate nucleotide sequences, and gen.seq.SNP is to generate
SNP sequences.
gen.seq.HKY(rooted.tree, pi, kappa, L, rate.scale = 1,
anc.seq = NULL)
gen.seq.SNP(rooted.tree, pi, L, rate.scale = 1, anc.seq = NULL)
rooted.tree |
a rooted tree in |
pi |
equilibrium probabilities, sums to 1. |
kappa |
transition and transversion bias. |
L |
number of sites. |
rate.scale |
a scale to all branch lengths. |
anc.seq |
an ancestral sequence either in nids or sids, length = L. |
The rooted.tree should be in a phylo class of ape,
and may be created by ms.
The pi has length 4 for nucleotide sequences, and 2 for SNP sequences.
The rate.scale is equivalent to rescale the height of
rooted.tree.
Return an object in Class seqgen.
Wei-Chen Chen wccsnow@gmail.com
Phylogenetic Clustering Website: http://snoweye.github.io/phyclust/
## Not run:
library(phyclust, quiet = TRUE)
# Generate a tree
set.seed(1234)
ret.ms <- ms(nsam = 5, nreps = 1, opts = "-T")
tree.ms <- read.tree(text = ret.ms[3])
# Generate nucleotide sequences
anc.HKY <- rep(0:3, 3)
pi.HKY <- c(0.2, 0.2, 0.3, 0.3)
kappa <- 1.1
L <- length(anc.HKY)
set.seed(1234)
paste(nid2code(anc.HKY, lower.case = FALSE), collapse = "")
(HKY.1 <- gen.seq.HKY(tree.ms, pi.HKY, kappa, L, anc.seq = anc.HKY))
# evolve 5 times longer
(HKY.2 <- gen.seq.HKY(tree.ms, pi.HKY, kappa, L,
rate.scale = 5, anc.seq = anc.HKY))
# Generate SNP sequences
anc.SNP <- rep(0:1, 6)
pi.SNP <- c(0.4, 0.6)
L <- length(anc.SNP)
set.seed(1234)
paste(sid2snp(anc.SNP), collapse = "")
(SNP.1 <- gen.seq.SNP(tree.ms, pi.SNP, L, anc.seq = anc.SNP))
# evolve 5 times longer
(SNP.2 <- gen.seq.SNP(tree.ms, pi.SNP, L, rate.scale = 5,
anc.seq = anc.SNP))
## End(Not run)