How do I read a doubled haploid population into R QTL using the read.cross function from mapmaker type of input (R version 3.2.1 and R/QTL version 1.38-4)
Rudie Antonise
The function read.cross fails to import the data (in mapmaker format) when I assign a DH population in the header of a mapmaker output. To solve this I used “bc” in the header of the file and crosstype=”dh” in the read.cross function. The genotypes are coded as “A’ and “B” in the original file. In this way I was able to loaded the file, but based on the QTL mapping results it seems that something is going wrong with the interpolation which seems to point to wrong assumptions / scores. I obtained I large signals when using the interval mapping method and almost no signal from marker regression. The crosstype loaded is a “doubled haploid” (checked by asking for crosstype).
When I re-code the original genotype data file to A/H instead of A/B following the same procedure the results seem much more sensible, comparable results for interval mapping and marker regression.
What is this the correct way to approach a DHs (using mapmaker format), to make sure the scores are loaded correct and obtain the correct estimated effects?
Karl Broman
I'd recommend calling it a backcross (and changing the genotype codes at the top to pretend that the BB's are hets) and then converting to doubled haploids afterwards.
mycross <- read.cross( .... )
class(mycross)[1] <- "dh"
karl
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Rudie Antonise
Op vrijdag 19 februari 2016 17:00:01 UTC+1 schreef Karl Broman: