This is an R Package for haplotype data simulation. Haplotypes are generated such that their allele frequencies and linkage disequilibrium coefficients match those estimated from an input data set. Montana (2005) describes the simulation algorithm. The figure shows some simulation results obtained from the ACE (angiotensin I converting enzyme) data set, included in the package. The upper triangular matrix represents the LD coefficients estimated from the real data, whereas the lower triangular matrix displays the corresponding LD in a small sample of haplotypes simulated with hapsim: the block-like LD structure of the real data is reproduced with high accuracy.
RequirementsThe R software for statistical computing (version 2+)
Current Version0.2 (released on Dec 13 2005)
Download, Installation and Usage
The simplest way to install hapsim is from within an R session (Packages -> Install Packages, then select "hapsim"), or download the files manually from CRAN. A manual is included in the distribution.
Montana G. (2005) HapSim: A simulation tool for generating haplotype data with pre-specified allele frequencies and LD patterns. Bioinformatics 21(23):4309-4311