Comments (3)
Hi Rui,
Thanks for your interest in QTLseqr.
The parameters are adjustable as in any function in R, just set windowSize = 1e5
etc.
However, I strongly advise to read the section of Magwene et al about window sizes - they should be in the realm of 20 cM and depending on your organism 100kb is typically considered small.
Finally, I'm sorry to say that QTLseqr only supports F2 and RIL populations for these types of analyses as it takes in to account the expected allele frequencies for these pops.
BC1 pops could be hypothetically but I have not coded these options in to the package.
Hope this helps,
Ben
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Rui,
You could conceivably run the QTLseq pipeline on a BC1 population with the F2 setting - just keep in mind that the way the confidence intervals are simulated assumes an F2 population. If you have a strong phenotype that you're selecting for then it should work and you will hypothetically still get a peak of deltaSNPindex ~0.5 for your locus.
Sorry but I am not planning on adding that functionality in the near future as I just dont have time.
Let me know if it works out.
Ben
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