Remove monomorphic loci, including those with all NAs
This script deletes monomorphic loci from a genlight {adegenet} object
gl.filter.monomorphs(x, verbose = NULL)
x |
– name of the input genlight object [required] |
verbose |
– verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log ; 3, progress and results summary; 5, full report [default 2, unless specified using gl.set.verbosity] |
A DArT dataset will not have monomorphic loci, but they can arise, along with loci that are scored all NA, when populations or individuals are deleted. Retaining monomorphic loci unnecessarily increases the size of the dataset and will affect some calculations.
Note that for SNP data, NAs likely represent null alleles; in tag presence/absence data, NAs represent missing values (presence/absence could not be reliably scored)
A genlight object with monomorphic ( and all NA) loci removed
Arthur Georges (Post to https://groups.google.com/d/forum/dartr)
# SNP data result <- gl.filter.monomorphs(testset.gl, verbose=3) # Tag P/A data result <- gl.filter.monomorphs(testset.gs, verbose=3)
Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.