R: The Main Function of phyclust for Sequencing Error Models

phyclust.se {phyclust} | R Documentation

## The Main Function of phyclust for Sequencing Error Models

### Description

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.

### Usage

    phyclust.se(X, K, EMC = .EMC, manual.id = NULL, byrow = TRUE)

### Arguments

`X` | nid/sid matrix with N rows/sequences and L columns/sites.
`K` | number of clusters.
`EMC` | EM control.
`manual.id` | manually input class ids.
`byrow` | advanced option for `X`, default = TRUE.

### Details

`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.

### Value

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:

`'SE'` | 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.

### Author(s)

Wei-Chen Chen wccsnow@gmail.com

### References

Phylogenetic Clustering Website: https://snoweye.github.io/phyclust/

### See Also

`.EMC`, `.EMControl`, `phyclust.se`, `phyclust.se.update`.

### Examples

    ## Not run:
    library(phyclust, quiet = TRUE)

    X <- seq.data.toy$org

    set.seed(1234)
    (ret.1 <- phyclust.se(X, 3))

    ## End(Not run)

[Package phyclust version 0.1-30 Index]