[R] infer haplotypes phasing trios tdthap

[Jing Hua Zhao]

Dear Tiago and David,

Just for a bit of personal interest, Haplin has been part of CRAN which is potentially helpful.

http://cran.r-project.org/web/packages/Haplin/index.html

from http://www.uib.no/smis/gjessing/genetics/software/haplin/

Best regards,


Jing Hua

-----Original Message-----
From: David Clayton [mailto:david.clayton at cimr.cam.ac.uk] 
Sent: 26 January 2009 10:07
To: Jing Hua Zhao
Cc: Tiago R Magalhães; r-help at R-project.org
Subject: Re: infer haplotypes phasing trios tdthap

tdthap wassn't intended to solve that problem and it has been removed 
from my own web site since I no longer consider it important enough to 
support.

DC



> 
> -----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
>