qtl2shiny Information

The popular R/qtl package for gene mapping has been redeveloped for high volume, multi-parent systems genetics data as R/qtl2. This new package is still in a state of flux, so please work with us to improve. Information in this folder largely refers to extensions to R/qtl2, including a Shiny interface.

http://www.statlab.wisc.edu/shiny/qtl2shiny shows this server in action. R/qtl2shiny Screen Shots has a series of screen shots, giving examples of R/qtl2shiny in action.

For more details on use of the package, see the R/qtl2shiny package, R/qtl2shiny User Guide and R/qtl2shiny Developer Guide. This document is created by inst/scripts/qtl2shiny_index.Rmd.

• R/qtl2shiny Package
• R/qtl2shiny Screen Shots
  • Screen Shots Markdown
  • Screen Shot Figures
• R/qtl2shiny User Guide
• R/qtl2shiny Developer Guide

See also ReclaDemo.Rmd for scripts to generate most of these summaries and figures. This uses four other packages that can be employed on their own separate from R/qtl2shiny. In particular, R/qtl2ggplot provides full capability for ggplot2 plot objects. The R/qtl2fst package transforms large, slow calc_genoprob objects central to R/qtl2 into a set of fst databases for quick access. R/qtl2pattern provides added funtionality to look at SNP patterns and other information in more detail. See each package for its own documentation.

• ReclaDemo.html & ReclaDemo.Rmd
• R/qtl2ggplot
• R/qtl2fst
• R/qtl2pattern

There is another package that is more specialized and still needs documentation: R/CausalMST concerns Causal Model Selection Tests, which are used in conjunction with mediation to formally infer causal relationship between a phenotype and other phenotypes that co-map.