How to filter loci?

[Ian Bremen]

Dear Karl, 

I got no clue how to filter loci?. i wat to omit/filter those loci from my dataset which have missing data more than 5%, since the manual talks about filtering individuals NOT the loci.

Regards, 

[Karl Broman]

You can use the function nmissing() to determine the number of missing genotypes at each marker.

   data(fake.f2)

   pmis <- nmissing(fake.f2, "mar") / nind(fake.f2)

You can then use drop.markers() to drop a set of markers, for example those with > 20% missing data.

  fake.f2.sub <- drop.markers(fake.f2, names(pmis)[pmis > 0.2])

karl