cM distance

[Tiago Ribeiro]

Hi,

I was having an issue loading all my markers (~6,600) to perform scantwo because it would complain that the vector was too long. 

Recently, I realized that the problem was the size of the chromosomes. I am working with Drosophila, chromosome X, 2 and 3. Chromosomes 2 and 3 are subdivided into 2L, 2R, and 3L, 3R for the left and right sides around the centromere. When I treat L and R as separate chromosomes, giving r/qtl 5 chromosome labels instead of 3, scantwo works normally.

Is there a problem with separating the chromosomes into 2 blocks? Does the cM distance between the markers influence their lod scores? 

Best,

[Martin Ferris]

Karl will have to confirm, but c should influence the a* and k* estimates between pairs of markers. I don't know what your recombination map looks like relative to the centromeres, but if you split the arms, it would really only affect LOD scores spanning the centromere, I think?

I've had issues with ~3700 markers across the Mouse genome (~2900 Mb on 20 chromosomes) in scantwo. I can't remember the exact problem, but I think the object just becomes too large to hold in Rs default memory allocation. I pruned the markers to (roughly) 1/5 Mb and it alleviated the problem. Be curious to serif you prune down, does that resolve it.

Regards,

Marty

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