Quantitative trait locus (QTL) analysis is a statistical method to link phenotypes with regions of the genome that affect the phenotypes in a mapping population. R/qtl is a powerful statistical program commonly used for analyzing rodent QTL crosses, but R/qtl is a command line program that can be difficult for novice users to run. J/qtl was developed as an R/qtl graphical user interface that enables even novice users to utilize R/qtl for QTL analyses. In this chapter, we describe the process for analyzing rodent cross data with J/qtl, including data formatting, data quality control, main scan QTL analysis, pair scan QTL analysis, and multiple regression modeling; this information should enable new users to identify QTL affecting phenotypes of interest within their rodent cross datasets.
- Quantitative trait locus analysis
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We are grateful to Sharon Tsaih and Qian Li for preparing the summary table and several figures.
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© 2009 Humana Press, a part of Springer Science+Business Media, LLC
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Smith, R., Sheppard, K., DiPetrillo, K., Churchill, G. (2009). Quantitative Trait Locus Analysis Using J/qtl. In: DiPetrillo, K. (eds) Cardiovascular Genomics. Methods in Molecular Biology™, vol 573. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60761-247-6_10
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-60761-246-9
Online ISBN: 978-1-60761-247-6
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