Here we consider a phenotype measured over time, and perform QTL analysis with each time point individually, to seek genetic loci that affect the response. The data concern a set of 162 recombinant inbred lines.

The top-left plot is a “heat map” of the LOD scores for each time point at each genomic position. LOD scores are also colored to indicate the sign of the QTL effect, with red indicating that BB lines have larger phenotype values and blue indicating that AA lines have larger phenotype values. We consider only those (position, time) pairs with LOD > 1.

When you hover over a point in the top-left plot, the LOD curves for the corresponding time are shown below, and the phenotype averages and estimated QTL effect (across time) for the corresponding genomic position are shown to the right.

Click on a point to show pointwise confidence bands on the QTL effect (± 2 SE). (We require a mouse click, as otherwise the graph was painfully slow to refresh.)

The code is on github.