Remove redundant markers

[shepher...@gmail.com]

Hello all,

I'm a beginner at using R, and I would like to construct a genetic map.

I have genotype data with about 17000 SNP markers. I followed the tutorial to drop markers with missing rates of more than 20%, then deleted duplicate markers and individuals, and markers with distorted segregation patterns.

After those processes, I still have about 5000 markers which causes inefficient computation. There was also an error when I tried to order markers after estimating the recombination fraction and forming linkage groups (the error message said "cannot allocate vector"), therefore I couldn't complete the remaining processes, such as calculating genetic distances, and QTL mapping.

I would like to remove redundant markers which are closer than 0.5 cm, is there any functions I can use? And how do I delete them without distance information?

Thanks a lot!

[Karl Broman]

There's a function findDupMarkers() for identifying markers with identical data.

There's also pickMarkerSubset(), for reducing to markers where no two adjacent markers are less than some distance apart, but for that you would need a map.

karl