switch.order removes pulled markers from cross

[Nathaniel Burner]

Hi Karl,

I pulled markers from a cross using pullCross. Later, I tried to switch the order of markers on a chromosome using

qtl = switch.order(qtl, chr =13, order = c(1:100, 106:110, 101:105, 111), error.prob = 0.0001, map.function = "kosambi")

The result was a cross with the switched marker orders, however the separate lists containing the pulled markers disappeared. Is there a way to retain these lists in the cross object?

Thanks,

Nathaniel

[Karl Broman]

pullCross appears to be an ASMap function. If it’s putting extra information in the cross object, the R/qtl functions are not guaranteed to retain that information.

karl