Assumes you have a data frame "x" which is the output from the rsq package from libsequence. These output look like:

sitei sitej rsq D Dprime
24 75 0.0123457 0.01 -1
24 186 1 0.09 1
24 246 0.0277778 0.02 -1
24 442 0.0123457 0.01 -1

Download example fasta and rsq output.

NOTE: Please make sure you have version 0.8.0 or newer of the analysis package. Several older versions had minor bugs that produce output which will give you garbled and nonsensical results with this R code.

The code uses equation 1 from Remington (2001) to estimate C via nonlinear least squares and then plot the decay of LD with distance and a heatmap of r^2.

run the function as LDit(x,n) where x is your dataframe with headers and n the sample size. Requires the lattice library.

Download LDit.r

References

Remington DL, Thornsberry JM, Matsuoka Y, Wilson LM, Whitt SR et al. (2001) Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proc Natl Acad Sci U S A 98: 11479-11484.

Tags: analysis