Volume measures for linkage disequilibrium
<p>Abstract</p> <p>Background</p> <p>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 the...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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BMC
2006-11-01
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| Series: | BMC Genetics |
| Online Access: | http://www.biomedcentral.com/1471-2156/7/54 |
| _version_ | 1818475522591555584 |
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| author | Lin Chia-Ho Chen Yuguo Sabatti Chiara |
| author_facet | Lin Chia-Ho Chen Yuguo Sabatti Chiara |
| author_sort | Lin Chia-Ho |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>We design a sequential importance sampling algorithm to evaluate volume measures on <it>I </it>× <it>J </it>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.</p> <p>Conclusion</p> <p>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.</p> |
| first_indexed | 2024-12-10T09:13:34Z |
| format | Article |
| id | doaj.art-7968f4cd7bc74dbebdd2d6deb01d3c49 |
| institution | Directory Open Access Journal |
| issn | 1471-2156 |
| language | English |
| last_indexed | 2024-12-10T09:13:34Z |
| publishDate | 2006-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genetics |
| spelling | doaj.art-7968f4cd7bc74dbebdd2d6deb01d3c492022-12-22T01:54:56ZengBMCBMC Genetics1471-21562006-11-01715410.1186/1471-2156-7-54Volume measures for linkage disequilibriumLin Chia-HoChen YuguoSabatti Chiara<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>We design a sequential importance sampling algorithm to evaluate volume measures on <it>I </it>× <it>J </it>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.</p> <p>Conclusion</p> <p>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.</p>http://www.biomedcentral.com/1471-2156/7/54 |
| spellingShingle | Lin Chia-Ho Chen Yuguo Sabatti Chiara Volume measures for linkage disequilibrium BMC Genetics |
| title | Volume measures for linkage disequilibrium |
| title_full | Volume measures for linkage disequilibrium |
| title_fullStr | Volume measures for linkage disequilibrium |
| title_full_unstemmed | Volume measures for linkage disequilibrium |
| title_short | Volume measures for linkage disequilibrium |
| title_sort | volume measures for linkage disequilibrium |
| url | http://www.biomedcentral.com/1471-2156/7/54 |
| work_keys_str_mv | AT linchiaho volumemeasuresforlinkagedisequilibrium AT chenyuguo volumemeasuresforlinkagedisequilibrium AT sabattichiara volumemeasuresforlinkagedisequilibrium |