Estimated QTL effects with CIM

[Nihal]

Hi Karl

I am using CIM in a backcross family. Could I use 'fitqtl' (and the
get.est=TRUE) in some form to get estimates of QTL effects of the
fitted CIM model? For the window size I used I can identify the
markers which are outside that for the position of putative QTL. Could
this be used in a 'covar' data.frame?

Thank you very much in advance.

Nihal

[Karl Broman]

Yes, you can use fitqtl to get estimates of QTL effects.

The specific markers chosen as covariates in CIM are saved as attributes to the output.
attr(myoutput, "marker.covar") gives the marker names and
attr(myoutput, "marker.covar.pos") gives their positions.

Consider the following example:

> data(hyper)
> hyper <- calc.genoprob(hyper, step=2.5)
> out <- scanone(hyper)
> out.cim <- cim(hyper, n.marcovar=3)
> attr(out.cim, "marker.covar")
[1] "D4Mit164" "D1Mit94" "D6Mit15"
> attr(out.cim, "marker.covar.pos")
chr pos
D4Mit164 4 29.5
D1Mit94 1 67.8
D6Mit15 6 66.7

karl

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