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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.