I am trying to use r-QTL with the new Multiple QTL Mapping functions. I know how to run the analysis and get the LOD profile, but I don't know how to analyse the results. I would like to get either a Bayes interval or a 1.5 LOD support interval, but the book I am using (A Guide to QTL Mapping with R/qtl) seems to indicate that both these functions assume a single QTL per trait. I would assume that with multiple QTL mapping you get multiple significant peaks and thus multiple intervals.
How do I extract these multiple intervals from my data?