Avoiding recomputation in linkage analysis
Schaffer AA, Gupta SK, Shriram K, Cottingham RW Jr
Human Heredity 1994 Jul-Aug;44(4):225-37
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 [Am J Hum Genet
1988;42:498-505]. The new method of handling loops extends a
proposal of Lange and Elston [Hum Hered 1975;25:95-105] 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.
back to link-compute