Creating Genetic map which follows the marker marker position and not start from 0cM

[Shameel Shah]

Dear Dr. Karl 

I wonder when making genetic map for individual chromosomes that have putative QTLs for instance on ch2, 5 and 10,  but the first genetic marker position starts at 26.2cM in this case R/qtl composes the genetic map from 0cM by using the first genetic marker and gives the value of 0cM when it is suppose to start from 26.2cM. This changes the whole genetic marker positions and reduces the confidence interval of the QTL position. Can this be altered in anyway to create a precise genetic map.  

Kind Regards

Shameel Shah. 

[Karl Broman]

Could you provide the exact code and results with an example of what you are concerned about?

karl

[Karl Broman]

I received the following email separately:

I have 3 putative QTLs on chr2, 5 and 10. I have made individual maps for chr's of interest, but for chr 2 the first marker position is 29.6cM however, the genetic map when constructed using R/qtl it scales and positions the first marker to 0cM. This changes the whole genetic marker positions on chr2 hence qtl position does not match.  Additionally, I want name the QTLs according to nomenclature but when I run the code it gives Q1, or Q2... is it possible to rename it. Lastly, I tried to post this question on google group but it seems not be not posting it. I am not sure why is this so, thus I am emailing you.

[Karl Broman]

Here's the figure that was attached.

[Karl Broman]

When you plot a map or qtl object, there is an argument "shift" that defaults to TRUE, in which case each chromosome is shifted so that it starts at 0 cM.

Also, makeqtl() has an argument qtl.name that allows you to indicate specific names.

Here's an example:

library(qtl)

data(hyper)

hyper <- calc.genoprob(hyper, step=1)
qtl <- makeqtl(hyper, chr=c(1,4), pos=c(20, 40), qtl.name=c("qtl_chr1", "qtl_chr4"), what="prob")

plot(qtl, shift=FALSE)

karl