Hi,
I've done QTL-Analysis using R/QTL. I would now like to find all the genes lying in the QTL-regions. Is there a function that will give me the positions of the flanking markers of the QTL-interval in my genetic map? So that I can say the QTL interval is from position x to position y and check the genes within this region.
Many thanks!
Nadia
Supposing you run scan1 (name of return object is data.scan1) on your data and want to get the 95% confidence interval (upper and lower marker) for the peak on chromosome 1, type
CI = bayesint(data.scan1, chr=1, prob=0.95)
lower_marker = find.marker(data, chr=CI[1,1], pos=CI[1,2])
lower_lod = CI[1,3]
print(paste("Lower marker:", lower_marker, "LOD:", lower_lod, sep=" "))
upper_marker = find.marker(data, chr=CI[3,1], pos=CI[3,2])
upper_lod = CI[3,3]
print(paste("Upper marker:", upper_marker, "LOD:", upper_lod, sep=" "))
Hi. Question: would this work also for composite-interval-mapping (CIM) ? Or how it can be calculated for CIM? Thanks
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