Hi Karl,
I've inquired about this issue before, but I'm hoping I've narrowed my question down enough to make it manageable. I'm stumped with my situation on chr2 determining how many of these peaks are actually independent. Via my unconfident analysis, it seems like there may just be 1 peak on chr2 @ 40cM, although there could very well be at least one more. I am especially suspicious because we have a candidate gene on chr2, corroborated by functional data that falls under the most distal peak on chr2. Anyway, I would be very grateful to have your guidance.
Scanone and scantwo analyses identify 3 loci on chr2 that may be QTL (attached).
When I consider the largest QTL (chr3) as a covariate, the most proximal peak on chr2 ('1' as I have it labeled) all but disappears and the LODs of the two more distal peaks on chr2 increase by ~50%. When I make chr2, peak '2' a covariate, the most proximal peak ('1') disappears and the most distal one ('3') is reduced. When I make chr2, peak '3' a covariate, the most proximal peak ('1') is reduced but still significant and peak 2 is barely significant.
Another approach I took was to build a multiple model, first just considering the middle peak ('2') on chr2, then running 'addqtl' and 'addpair'.
Here's the addqtl with the chr2 locus included. It doesn't look like there's much solid evidence for an added QTl on chr2, although there seems to be weak evidence for a QTL on chr4.
> mod3_add <- addqtl(std_210928, qtl = mod3_refined, formula = y~Q1+Q2+Q3+Q4+Q5, pheno.col = "std")
> summary(mod3_add)
chr pos lod
c1.loc43 1 43.0 3.096
c2.loc55 2 55.0 2.632
c3.loc46 3 46.0 2.595
c4.loc16 4 16.0 4.602
c5.loc40 5 40.0 2.882
6.28 6 39.9 2.312
7.015 7 20.1 0.833
Here's addpair without the chr2 locus included to see if 2 loci should be added to chr2. Again, not much evidence for 2 QTL on chr2 from what I can tell.
mod3_ap <- addpair(std_210928, qtl = mod3_refined, chr = 2, formula = y~Q1+Q3+Q4+Q5, pheno.col = "std")
Scanning full model for chr 2 and 2
Scanning add've model for chr 2 and 2
> summary(mod3_ap)
pos1f pos2f lod.full lod.fv1
lod.int pos1a pos2a lod.add lod.av1
c2:c2 40 54 27.5 4.25 1.59 41 54 25.9 2.65
Thank you for any guidance you can give here.
Jason