R qtl2: Rewrite of a very old R package - Karl Broman

For nearly 20 years, I've been developing, maintaining, and supporting an R package, R/qtl, for mapping quantitative trait loci (genetic loci that contribute to variation in quantitative traits, such as blood pressure) in experimental crosses (such as in mice). It's a rather large package, with 39k lines of R code, 24k lines of C code, and nearly 300 user-accessible functions. In the past several years, I've been working on rewriting the package, to better handle high-dimensional data and more complex experimental crosses. This has been a good opportunity to take advantage of many new tools, including Rcpp, Roxygen2, and testthat. I'll describe my efforts to avoid repeating the mistakes I made the first time around.

About the Author

Karl Broman

Karl Broman is Professor in the Department of Biostatistics & Medical Informatics at the University of Wisconsin–Madison; research in statistical genetics; developer of R/qtl (for R). Karl received a BS in mathematics in 1991, from the University of Wisconsin–Milwaukee, and a PhD in statistics in 1997, from the University of California, Berkeley; his PhD advisor was Terry Speed. He was a postdoctoral fellow with James Weber at the Marshfield Clinic Research Foundation, 1997–1999. He was a faculty member in the Department of Biostatistics at Johns Hopkins University, 1999–2007. In 2007, he moved to the University of Wisconsin–Madison, where he is now Professor. Karl is a Senior Editor for Genetics, Academic Editor for PeerJ, and a member of the BMC Biology Editorial Board. Karl is an applied statistician focusing on problems in genetics and genomics – particularly the analysis of meiotic recombination and the genetic dissection of complex traits in experimental organisms. The latter is often called “QTL mapping.” A QTL is a quantitative trait locus – a genetic locus that influences a quantitative trait. Recently he has been focusing on the development of interactive data visualizations for high-dimensional genetic data; see his R/qtlcharts package and his D3 examples.

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