How to get the beginning and end-positions of a QTL-interval after doing QTL-analysis with R/QTL?
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6.6 years ago
nx8 ▴ 10

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

R QTL R/QTL QTL-Analysis QTL-interval • 2.5k views
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4.8 years ago
Matthias ▴ 50

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=" "))
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Hi. Question: would this work also for composite-interval-mapping (CIM) ? Or how it can be calculated for CIM? Thanks

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