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.clay...@cimr.cam.ac.uk] Sent: 26 January 2009 10:07 To: Jing Hua Zhao Cc: Tiago R Magalhães; r-help@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:tiag...@gmail.com] > Sent: 22 January 2009 11:10 > To: r-help@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 > ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
