QTLRel: an R package for genome-wide association studies in which relatedness is a concern.
QTLRel: an R package for genome-wide association studies in which relatedness is a concern.
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DOI：
10.1186/1471-2156-12-66
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发表时间：
2011-07-27
期刊：
影响因子：
2.9
通讯作者：
Skol AD
中科院分区：
文献类型：
--
作者：
Cheng R;Abney M;Palmer AA;Skol AD
现有的数量性状作图软件要么不能模拟多基因变异，要么不允许纳入一个以上的遗传方差分量。对受试者之间的遗传相关性建模不当可能导致过多的假阳性。我们已经开发了一个R包，QTLRel，使遗传相关性以及协变量和非遗传方差分量的建模更加灵活。我们已经成功地使用该软件包分析了许多数据集，包括F34体重数据，其中包含688个个体在3105个SNP标记处进行基因分型，并确定了11个QTL。在配备2.40 GHz Intel（R）Core（TM）2 Quad CPU的Linux机器上，估计方差分量花费了295秒，执行基因组扫描花费了70秒。QTLRel为全基因组关联研究提供了一个工具包，该工具包能够计算来自系谱的遗传发生率矩阵、估计方差分量、执行基因组扫描、合并交互式协变量以及遗传和非遗传方差分量，以及其他功能，如多QTL作图和全基因组上位性。
Existing software for quantitative trait mapping is either not able to model polygenic variation or does not allow incorporation of more than one genetic variance component. Improperly modeling the genetic relatedness among subjects can result in excessive false positives. We have developed an R package, QTLRel, to enable more flexible modeling of genetic relatedness as well as covariates and non-genetic variance components. We have successfully used the package to analyze many datasets, including F34 body weight data that contains 688 individuals genotyped at 3105 SNP markers and identified 11 QTL. It took 295 seconds to estimate variance components and 70 seconds to perform the genome scan on an Linux machine equipped with a 2.40GHz Intel(R) Core(TM)2 Quad CPU. QTLRel provides a toolkit for genome-wide association studies that is capable of calculating genetic incidence matrices from pedigrees, estimating variance components, performing genome scans, incorporating interactive covariates and genetic and non-genetic variance components, as well as other functionalities such as multiple-QTL mapping and genome-wide epistasis.
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影响因子：
3.8
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