###Note: feel free to try v.64 if you are intrested in the new LDnClustering implementation (Li, Z., Kemppainen, P., Rastas, P., Merila, J. Linkage disequilibrium clustering-based approach for association mapping with tightly linked genome-wide data. Accepted to Molecular Ecology Resources)
Linkage disequilibrium (LD) network analysis (LDna) can be used to find clusters of loci in high LD from population genomic data sets using network analysis. It provides a means to partition population genomics data into sets of loci that bear similar population genetic signals. It can for instance be used to in silico identify inversion polymorphism and loci involved in local adaptation. As it only requires a matrix of pair-wise LD values it is particularly useful for non-model species where closely related and well-characterized reference genomes are not available.
Reference: http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12369/abstract
Current beta version is 0.60.
Any questions or suggestions may be posted at: https://groups.google.com/forum/#!forum/ld-network-analysis
###Installing
With devtools (accessible from CRAN) LDna can be installed by:
devtools::install_github("petrikemppainen/LDna")This downloads the source directly from github and builds the vignettes and thus requires LaTeX to be installed on your computer.
Alternatively, download the source file (LDna_0.60.tar.gz) directly and install by:
install.packages("/path_to/source_file", repos = NULL, type = "source")Please install and follow package documentation (includes two tutorials) for more information.