Avoiding Recomputation in Linkage Analysis

Alejandro Alberto Schäffer, Sandeep Kumar Gupta, K. Shriram, Robert W. Cottingham Jr

Human Heredity, 1994

Abstract

We describe four improvements we have implemented in a version of the genetic linkage analysis programs in the LINKAGE package: subdivision of recombination classes, better handling of loops, better coordination between the optimization and output routines, and a checkpointing facility. The unifying theme for all the improvements is to store a small amount of data to avoid expensive recomputation of known results. The subdivision of recombination classes improves on a method of Lathrop and Lalouel [Amer. J. Hum. Genetics 42(1988), pp. 498--505]. The new method of handling loops extends a proposal of Lange and Elston [Hum. Hered. 25(1975), pp. 95--105] for loopless pedigrees with multiple nuclear families at the earliest generation. From a practical point of view, the most important improvement may be the checkpointing facility which allows the user to carry out linkage computations that are much longer than the mean-time-to-failure of the underlying computer.

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