haplo.post.prob {phyclust} | 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 |
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:
| |||||||||||||
'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
See Also
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)