QTLRel is an R package for mapping quantitative trait loci (QTLs) in experimental crosses such as advanced intercross lines (AILs) where relatedness among individuals should not be ignored.
QTLRel includes functions to estimate background genetic variance components, impute missing genotypes, simulate genotypes, perform a genome scan for quantitative trait loci, and plot the mapping results.
R code to select breeders from an advanced intercross line so that they minimize inbreeding in the offspring.
Demonstration of QTL mapping for fear conditioning traits in LG/J x SM/J mouse advanced intercross line. Contains data and R to reproduce results of a forthcoming Genetics paper.
QTL mapping for prepulse inhibition phenotypes in F1 panel derived from common inbred mouse strains using a linear mixed model (GEMMA). Contains data and R code to reproduce results of upcoming GWAS manuscript.
* dbGaP Study: “Sensitivity to the Subjective Effects of Amphetamine”
Study results and data sets available for examination and analysis.
The goal of this study was to identify SNPs associated with subjective, physiological, and behavioral responses to d-amphetamine. Molecular data included whole-genome genotyping (AFFY_6.0 platform) and imputation (1000 Genomes Project). This project was a collaboration with Harriet de Wit, Director of the Human Behavioral Pharmacology Lab.