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
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