[R] infer haplotypes phasing trios tdthap

[Jing Hua Zhao]

Dear Tiago,

I received this message from r-help. I should say I have limited experiences with tdthap so David should have the final say about it? Alternatively, you may wish to use independent programs as listed in the linkage server at Rockefeller?

I would of course find out if I have miscopied David's original code!

Many thanks,


Jing Hua

-----Original Message-----
From: Tiago R Magalhães [mailto:tiago17 at gmail.com] 
Sent: 22 January 2009 11:10
To: r-help at R-project.org
Subject: infer haplotypes phasing trios tdthap

Dear R mailing list,

I have a dataset with genotypes from trios and I would like to infer 
haplotypes for each mother, father and child. The package that I could 
find that can do this is tdthap.

But when the mother is homozygous (e.g., 2/2) the haplotype is called as 
not possible to infer (0); I would prefer for it to call the genotype 
(2). From what I understand it is doing what I would like for the father 
(example below).

Can anyone provide me with some information about this tdthap behaviour? 
And is there any other package that would do this? (Searched for it, 
couldn't find it)

Thank you very much,

Tiago Magalhães



example (ped file with pedigrees)
9 100 102 101 1 2 1 1 2 1 2 2 1 2
9 101 0 0 2 1 1 1 2 1 2 2 2 2
9 102 0 0 1 1 2 1 2 1 2 2 1 1


data out: hap.transmit(example)

ped    id    father    mother
9      100    102       101

f.tr.1    f.tr.2    f.tr.3    f.tr.4   
1         0           2          1

m.tr.1    m.tr.2    m.tr.3    m.tr.4
   0        0         0          0