Haplotype Phasing / Genotyping In R

Question

[John]

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 ----

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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).

Answer 1

[Genotepes]

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