R: Tzeng's Method: Finding the Best Number of Clusters

getcut.fun {phyclust} | R Documentation

## Tzeng's Method: Finding the Best Number of Clusters

### Description

For SNP sequences only, Tzeng's method (2005) uses an evolution approach to group haplotypes based on a deterministic transformation of haplotype frequency. This function find the best number of clusters based on Shannon information content.

### Usage

    getcut.fun(pp.org, nn, plot = 0)

### Arguments

`pp.org` | frequency of haplotypes, sorted in decreasing order.
`nn` | number of haplotypes.
`plot` | illustrated in a plot.

### Details

`pp.org` is summarized from `X` in `haplo.post.prob`, `nn` is equal to the number of rows of `X`.

This function is called by `haplo.post.prob` to determine the best guess of number of clusters. See Tzeng (2005) and Shannon (1948) for details.

### Value

Return the best guess of number of clusters.

### Author(s)

Jung-Ying Tzeng.

Maintain: Wei-Chen Chen wccsnow@gmail.com

### References

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

Tzeng, J.Y. (2005) “Evolutionary-Based Grouping of Haplotypes in Association Analysis”, Genetics Epidemiology, 28, 220-231. http://www4.stat.ncsu.edu/~jytzeng/software.php

Shannon, C.E. (1948) “A mathematical theory of communication”, Bell System Tech J, 27, 379-423, 623-656.

### See Also

`haplo.post.prob`.

### Examples

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

    data.path <- paste(.libPaths()[1], "/phyclust/data/crohn.phy", sep = "")
    my.snp <- read.phylip(data.path, code.type = "SNP")
    ret <- haplo.post.prob(my.snp$org, ploidy = 1)
    getcut.fun(sort(ret$haplo$hap.prob, decreasing = TRUE),
               nn = my.snp$nseq, plot = 1)

    ## End(Not run)

[Package phyclust version 0.1-30 Index]