I know that linkage disequilibrium could be calculated using certain software, such as GENEPOP. However, I would appreciate your answer about whether using a 2*2 table that combines allele and haplotype frequencies to calculate the statistics related to linkage disequilibrium is precise and accurate.
Thanks a lot in advance!
Why not use a R package instead (http://cran.r-project.org/web/views/Genetics.html)! This would not only give you manual but is also precise in its calculation.
Thank you Akshay, but when I downloaded the files, I could not find that for set-up. I do not know what the problem is.
I reckon, just downloading won't help. You will have to either install the library from the downloaded package or connect R software directly to the CRAN package through the package manager. A brief tutorial is mentioned here (http://math.usask.ca/~longhai/software/installrpkg.html) and (http://stackoverflow.com/questions/2169118/installing-all-cran-packages-that-are-not-already-installed). The installation also is OS depended.
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