\name{pair.result.ld.snp} \alias{pair.result.ld.snp} %- Also NEED an '\alias' for EACH other topic documented here. \title{ Function to calculate the pairwise D', $r^2$, LOD of a pair of specified SNPs} \description{ \code{pair.result.ld.snp.Rd} calculates the pairwise D', $r^2$, LOD of a pair of specified SNPs in a \code{snp.matrix} object. This is used mainly for debugging. } \usage{ pair.result.ld.snp(snpdata, loc.snpA, loc.snpB) } %- maybe also 'usage' for other objects documented here. \arguments{ \item{snpdata}{An object of \code{snp.matrix} class with M samples of N snps} \item{loc.snpA}{index of the first snp; should be between 1 and N} \item{loc.snpB}{index of the second snp; should be between 1 and N} } \value{ Returns nothing. Results are displayed in stdout/console. } \references{ Clayton, D.G. and Leung, Hin-Tak (2007) An R package for analysis of whole-genome association studies. \emph{Human Heredity} \bold{64}:45-51.\cr GSL (GNU Scientific Library) \url{http://www.gnu.org/software/gsl/} } \author{Hin-Tak Leung \email{htl10@users.sourceforge.net}} \note{ Not really recommended for daily usage; the result isn't saved anywhere and this routine is primarily for debugging the details and correctness of the calculation. } \seealso{\code{\link{snp.matrix-class}}} \examples{ data(testdata) pair.result.ld.snp(Autosomes, 1, 2) } \keyword{htest} \keyword{models} \keyword{dplot}