I am looking for R package that can reconstruct phase and output in single nucleotide polymorphism markers. I can see discussion on non R package - in previous posts but I could not find appropriate package to do in R.... .......
individual genotypes
A1A1 B1B1, A1A2 B1B2, A1A1 B2B2, A1A2 B1B2
potential haplotype alleles - hap1 (A1B1), hap2 (A1B2) ,
hap3 (A2B1), hap4 (A2B2)
individual haplotype genotype = hap1 / hap1, hap1 / hap4,
hap2 / hap 2, hap1 / hap4
---- depends upon phase ----
======
Here is small datafile
set.seed (14)
pool = sample (c("AA","AB", "BB"), 1000, replace = T)
mydf <- data.frame (M1= pool[1:100], M2= pool[101:200], M3= pool[201:300])
I tried hapassoc it do haplotype association but doesnot output the two haplotypes (haplotype reconstruction).
1 answer
Hi
I think haplo.score from Schaid's team (or people around Schaid) is doing this. This is not really explicit as their main focus is around testing association but you can have a summary() function which gives the probabilities for each haplotype.
You need some scripting to choose which haplotype you want for each individual (random based on posterior probabilities, most likely, less likely - why not ? ..).
Best
Christian
http://mayoresearch.mayo.edu/mayo/research/schaid_lab/software.cfm
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