Here, we upload all necessary files for the example of an application of LDJump.
The required R-command for the estimation of the recombination map with LDJump for the recombination map with a background rate of 0.054 is the following:
require(LDJump) results = LDJump("/pathToSample/HatLandscapeN16Len1000000Nrhs15_th0.01_540_1.fa", alpha = 0.05, segLength = 1000, pathLDhat = "/pathToLDhat", format = "fasta", refName = NULL, thth = 0.01) postscript("Results.eps", horiz = F) plot(results[], xlab = "Segments", ylab = "Estimated Recombination Rate", main = "Estimated recombination map with LDJump") dev.off()
With the plot-Function of the package stepR one will obtain the estimated map with the estimated recombination rates plotted on the y-axis and the according segment number on the x-axis. The postscript and dev.off commands before and after plotting the results, respectively, will save the result in EPS-format.
LDJump returns a list of 7 elements which contains the estimated recombination map, the constant recombination rate estimates per segment, the calculated summary statistics (in a matrix), the type I error probability, the sample size, the sequence length and the segment lenght used. For a constant recombination rate estimation only the latter six elements are returned.
Notes: Both ZIP-Files have to be unzipped before usage in the R-function LDJump. Runtime of one of these examples will be at least one hour. We recommend when LDJump is applied with different populations/examples simultaneously to create directories and start LDJump* separately from these directories.
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