haplo.post.prob: 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

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.

number of clusters.

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.

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.

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

Examples

Run this code

# 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)
# }

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