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7.1 Introduction to lm_auto and lm_pval

The programs, lm_auto and lm_pval, and the three programs in the following chapter, see Estimating Location LOD Scores by MCMC, are referred to as "Autozyg" programs. These use MCMC sampling of the meiosis indicators, S, which determine autozygosity (ibd). They all use the LM-sampler (a combination of locus (L) and meiosis (M) block Gibbs MCMC samplers of S).

lm_auto uses the LM-sampler to realize ibd configurations from their posterior distribution given the marker data. Given marker data, it estimates conditional probabilities of genome sharing patterns (gene ibd) among specified haplotypes, usually from affected individuals. The marker data are used jointly in the sampling, but the resulting ibd is scored marginally at each marker locus.

lm_pval also uses LM-sampling to provide the conditional distribution of an ibd measure given marker data. In principle it can be used to provide Monte Carlo estimates of any NPL (Non-Parametric Linkage) statistics for detecting linkage. Trait information provided to the program consists of the list of affected members of the pedigree.



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