haplo.post.prob: Tzeng's Method: Haplotype Grouping for SNP Sequences
In snoweye/phyclust: Phylogenetic Clustering (Phyloclustering)

haplo.post.prob

R Documentation

Tzeng's Method: Haplotype Grouping for SNP Sequences

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 is a modified version of original function, haplo.score.RD.unphased.fun.

Usage

  haplo.post.prob(X, ploidy = 2, skip.haplo = 1e-07, K = NULL)

Arguments

`X`	sid matrix with `N` rows/sequences and `L` columns/sites.
`ploidy`	ploidy, no effect for phase known, keep consistence only.
`skip.haplo`	lower bound of haplotypes frequencies.
`K`	number of clusters.

Details

X should be a phase known haplotype data. For phase unknown and Tzeng's method (2006) are not tested yet.

If K is NULL, the result of getcut.fun will be used.

Value

See the original paper and source codes' documents for details. The function returns a list contains:

'haplo'

summarized data set in a list contains:

'haplotype'	unique haplotypes, dim = `N_{unique} \times L`.
'hap.prob'	frequency of haplotypes.
'post'	posterior probabilities of phase unknown haplotypes.
'hap1code'	unique ids of 'haplotype'.
'hap2code'	unique ids of 'haplotype', no effect if ploidy = 2.
'indx.subj'	id of subjects.

'FD.id'

unique ids of 'haplotype' for full dimension analysis.

'RD.id'

unique ids of 'haplotype' for reduced dimension analysis.

'FD.post'

posterior probabilities for full dimension analysis.

'RD.post'

posterior probabilities for reduced dimension analysis.

'g.truncate'

number of clusters

ToDo(s)

test codes for phased unknown cases.

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. https://www4.stat.ncsu.edu/~jytzeng/software.php

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)
str(ret)

## End(Not run)

snoweye/phyclust documentation built on Sept. 12, 2023, 5 a.m.