The phyclust.se is an advanced function of phyclust.
The phyclust.se implements finite mixture models for sequence data
with sequencing errors. The same as phyclust,
the mutation processes are modeled by evolution processes based on
Continuous Time Markov Chain theory.
phyclust.se(X, K, EMC = .EMC, manual.id = NULL, byrow = TRUE)A list with class phyclust will be returned containing
several elements as described in phyclust. But, the
phyclust.se returns extra parameters for sequencing errors, and
they are shown in the following:
a list returning parameters of sequencing error models, including:
| 'type' | 'TRUE' for modeling sequencing errors. |
| 'model' | 'CONVOLUTION', the only model implemented. |
| 'constant' | the constrained constant for sequencing errors. |
| 'f.err' | probability matrix, each row sums to 1. |
nid/sid matrix with \(N\) rows/sequences and \(L\) columns/sites.
number of clusters.
EM control.
manually input class ids.
advanced option for X, default = TRUE.
Wei-Chen Chen wccsnow@gmail.com
phyclust.se considers mutations with sequencing error, but only
for NUCLEOTIDE data and only the EM algorithm is
implemented. Currently, phyclust.se implements the following steps:
| 1 | assume non-sequencing errors as the phyclust does. |
| 2 | use the initialization as the phyclust does. |
| 3 | run the phyclust to find the non-sequencing error MLE's. |
| 4 | initial by the results of phyclust. |
| 5 | update all parameters including probabilities of sequencing errors. |
See the help page of phyclust for the explanations of
input arguments since both functions share the same arguments. Note that
the underling model assumptions are very different of both functions.
Phylogenetic Clustering Website: https://snoweye.github.io/phyclust/
.EMC,
.EMControl,
phyclust.se,
phyclust.se.update.
if (FALSE) {
library(phyclust, quiet = TRUE)
X <- seq.data.toy$org
set.seed(1234)
(ret.1 <- phyclust.se(X, 3))
}
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