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SOFTWARE Open Access QTLRel: an R Package for Genome-wide
 

Summary: SOFTWARE Open Access
QTLRel: an R Package for Genome-wide
Association Studies in which Relatedness
is a Concern
Riyan Cheng1
, Mark Abney1
, Abraham A Palmer1,2*
and Andrew D Skol3
Abstract
Background: 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.
Results: 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.
Conclusions: 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

  

Source: Abney, Mark - Department of Human Genetics, University of Chicago

 

Collections: Computer Technologies and Information Sciences; Biology and Medicine