Question: Pi_Hat and pedigree
0
gravatar for jzannatun
4 months ago by
jzannatun0
jzannatun0 wrote:

I am new in this field. Can anyone kindly tell me the process of making the pedigree tree of family pairs based on their pi_hat value? Any suggestions of software or programming languages are highly appreciable. Thank you in advance.

R software error • 239 views
ADD COMMENTlink modified 17 days ago • written 4 months ago by jzannatun0
1

Just the pi hat value? That's too little information. You can guess the pi-hat range if the pedigree relationship is known, or use the pi-hat among other data points to correct a wrongly attributed relationship, but without sex information, Z0 Z1 Z2 values and as much of such information as can be made available, making a pedigree is nearly impossible. How would you even figure out which groups cluster into families? Caveat emptor - machine learning could probably do it but I don't know if that technology exists yet

ADD REPLYlink written 4 months ago by RamRS20k

And why is this tagged R and software error? This is neither - you're probably using KING or PLINK's --rel-check or --genome options. This is most definitely not a software error. Please use relevant tags and more importantly, avoid irrelevant ones.

ADD REPLYlink written 4 months ago by RamRS20k
0
gravatar for jzannatun
17 days ago by
jzannatun0
jzannatun0 wrote:

Dear RamRS thank you for your reply. I used R to make pedigree tree of family pairs with their given pi_hat value using "igraph" package of R. I will avoid the irrelevant tags next time.

ADD COMMENTlink written 17 days ago by jzannatun0
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