Plotting all LOD scores and markers

[Rachel Tavares]

Hello,

After running composite interval mapping, I used the plot(scan.mapthis) function and the plot produced points only for the highest LOD score marker on each chromosome. I would like to have a plot with all of them. Is this possible? I have 42,868 markers so it is large. 

Thank you!

Rachel Tavares 

[Karl Broman]

Can you show the code you used to create the scan.mapthis object?

I should be that if you use plot( ) with the output of cim( ), it will show the LOD curves across the whole genome, just as with the output of scanone( ).

karl

[Rachel Tavares]

mapthis <- calc.genoprob(mapthis, step = 0, off.end = 0.0, error.prob = 0.001, stepwidth = "fixed", map.function = "kosambi")

scan.mapthis <- cim(mapthis, pheno.col = 1, method = "hk", map.function = "kosambi")

plot(scan.mapthis)

I viewed the scan.mapthis and it does have many many markers on each chromosome with representing LOD scores. The plot however just shows the highest LOD score from each chromosome instead of them all. 

[Karl Broman]

I don't know what could be going wrong. If you try the following example, does it look correct?

    library(qtl)

    data(hyper)
    hyper <- calc.genoprob(hyper, step=1)
    out_cim <- cim(hyper, method="hk")
    plot(out_cim)

Maybe there are a bunch of missing values in the scan.mapthis output?

    sum(is.na(scan.mapthis[,3]))

karl