I have two SNPs from FTO gene and i want to analysis their LD with R analysis. How to calculate r^2 for these two SNPs? I have already calculate the D' with script LD (rs1421085, rs9939609) and i get the result :
Pairwise LD
-----------
D D' Corr
Estimates: 0.1815744 0.9437594 0.9187018
X^2 P-value N
LD Test: 79.33722 0 47
I don't quite understand with reading and intrepretating this data. Please help me11
Hello Rut,
If I am not mistaken, you are using the ‘genetics’ package from Gregory Warnes. If this is the case in the output you provided the first-row last column (Corr) is the correlation coefficient between the markers (r). R^2, in this case, would be 0.9187018^2 or 0.844013. I have also attached the package documentation if it is of use to you.
Hope this helps,
Andric
Hi Andric, thank you for your explanation. Previously i have thought like you too. But since i'm not sure, i want to search any other explanation. But it' already clear. Thank you
Hi,
can anybody please tell me how to prepare the tetraploid SNP data set to be able to calculate LD by using genetics package in r.
Thanks
- Badges
- Science topic
- Similar topics
- Biological Science
- Biochemistry
- Biomolecules
- Nucleic Acids
- RNA
- Small RNA
- microRNA