Order of markers_BC2S1 population

[Varvara Marinopoulou]

Dear Karl,

I am constructing a genetic map for a BC2S1 population of tomato, consisting of 300 markers and 153 individuals. As the  physical positions of the markers are known,  I have ordered them according to their positions in Mbp, in the input file. Using the rf matrix (rf <- pull.rf(mydata)), I checked the recombination frequences among pairs of markers, and based on them, the order must be changed in the genetic map. 

I thought that the order of markers in the genetic map we get as output from R would be based on the recombination fractions among pairs of markers and not on the order of markers used in the input file. 

I have tried to use orderMarkers() and ripple() functions but I get a warning message that they are not available for bcsft type of poupulation, as mine.

Is there any way in R/qtl, to order the markers based on the recombination fractions among them?

Thank you in advance.

Best regards,

Varvara

PS: In the input file I have indicated the number of linkage group to which each of the markers belongs. Their positions in Mbp is not indicated. The order of markers is based on their physical positions on the chromosomes.

[Karl Broman]

If you have a particular order you want to switch to, you can use switch.order() to change to that order. 

You could try treating the cross as an f2 rather than bc2f1.

karl