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Volume measures for linkage disequilibrium.

ABSTRACT:

Background

Defining measures of linkage disequilibrium (LD) that have good small sample properties and are applicable to multiallelic markers poses some challenges. The potential of volume measures in this context has been noted before, but their use has been hampered by computational challenges.

Results

We design a sequential importance sampling algorithm to evaluate volume measures on I x J tables. The algorithm is implemented in a C routine as a complement to exhaustive enumeration. We make the C code available as open source. We achieve fast and accurate evaluation of volume measures in two dimensional tables.

Conclusion

Applying our code to simulated and real datasets reinforces the belief that volume measures are a very useful tool for LD evaluation: they are not inflated in small samples, their definition encompasses multiallelic markers, and they can be computed with appreciable speed.

SUBMITTER: Chen Y

PROVIDER: S-EPMC1665459 | biostudies-literature | 2006 Nov

REPOSITORIES: biostudies-literature

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Volume measures for linkage disequilibrium.

Chen Yuguo Y Lin Chia-Ho CH Sabatti Chiara C

BMC genetics 20061117

<h4>Background</h4>Defining measures of linkage disequilibrium (LD) that have good small sample properties and are applicable to multiallelic markers poses some challenges. The potential of volume measures in this context has been noted before, but their use has been hampered by computational challenges.<h4>Results</h4>We design a sequential importance sampling algorithm to evaluate volume measures on I x J tables. The algorithm is implemented in a C routine as a complement to exhaustive enumera ...[more]

PMID: 17112381

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