title: Quantitative trait locus analysis using J/qtl.
abstract: 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.
authors.affiliation: The Jackson Laboratory, Bar Harbor, ME, USA.
authors.forename: Randy
authors.initials: R
authors.lastname: Smith
authors.forename: Keith
authors.initials: K
authors.lastname: Sheppard
authors.forename: Keith
authors.initials: K
authors.lastname: DiPetrillo
authors.forename: Gary
authors.initials: G
authors.lastname: Churchill
mesh_terms: D000465:Algorithms; D000818:Animals; D002874:Chromosome Mapping / Q000379:methods*; D006801:Humans; D011786:Quality Control; D040641:Quantitative Trait Loci / Q000235:genetics*; D012044:Regression Analysis; D012984:Software