Does R/qtl calculates precise and correct position of the marker?

[Shameel Shah]

Dear Dr Karl

I found an interesting thing while using r/qtl to create the genetic map. 

The marker position that I am using for calculation is not an exact but close approximate using database for rice sequence. Whilst making the genetic map for chromosome 10 I found out that genetic map generated by using approximate marker position uses the same values as I input into the dataset. It does not check nor corrects the marker position to the exact locations within the chromosome. So, I used Antmap software to calculate the accurate positions and locations of each marker. Then I used Antmap cM position data in R/qtl to make genetic map which then outputted the right map with right marker positions and its locations on the chromosome.   

I have attached the result for my chr10 genetic map using Antmap and then right genetic map using r/qtl

With Respect

Shah

[Karl Broman]

If you estimate a map with est.map(), you need to use replace.map() to plug it back into the cross object.

Here's an example:

library(qtl)
data(hyper)
newmap <- est.map(hyper, error.prob=0.01, map.function="c-f")
hyper <- replacemap(hyper, newmap)

karl