How can multiple crosses be combined?
c.cross to combine multiple backcrosses and/or intercrosses, provided that they have the same genetic maps. This should be done after running calc.genoprob or sim.geno The combined analysis of multiple crosses requires care and is beyond the scope of this book. • Can one apply the “False discovery rate” (FDR) idea to QTL mapping with R/qtl? In the context of a single phenotype, one cannot fruitfully apply the false discovery rate idea to QTL mapping. If one views as the set of null hypotheses that individual loci are not linked to any QTL, one really has just one null hypothesis per chromosome, and so a total of 20 null hypotheses for the mouse genome. • Can R/qtl be used to perform association mapping (aka in silico mapping)? No. • Can one use physical locations of markers in place of a genetic map? The results of QTL analysis depend critically on the order of the genetic markers, and so knowledge of the physical locations of markers will be useful. However, calculations of conditiona
