Example/Example_Readme.md

In PhHermann/LDJump: Estimating Variable Recombination Rates from Population Genetic Data

Example

Here, we upload all necessary files for the example of an application of LDJump.

• SimulatedPopulations.zip: This file contains three different simulation setups of 16 individuals (=sequences) with background rates of 0.001, 0.0054, and 0.001. This setup contains 15 Hotspots of 8 to 40 folds of the background rates evenly distributed across the sequence.

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", pathPhi = "/pathToPhi", format = "fasta", refName = NULL)
postscript("Results.eps", horiz = F)
plot(results[[1]], 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.

PhHermann/LDJump documentation built on Nov. 16, 2019, 12:53 p.m.