This function uses the statistic set in the parameter stat.keep from
function gl.report.ld.map to choose the SNP to keep when two
SNPs are in LD. When a SNP is selected to be filtered out in each pairwise
comparison, the function stores its name in a list. In subsequent pairwise
comparisons, if the SNP is already in the list, the other SNP will be kept.
gl.filter.ld(
x,
ld.report,
threshold = 0.2,
pop.limit = ceiling(nPop(x)/2),
verbose = NULL
)The reduced genlight object.
Name of the genlight object containing the SNP data [required].
Output from function gl.report.ld.map
[required].
Threshold value above which loci will be removed [default 0.2].
Minimum number of populations in which LD should be more than the threshold for a locus to be filtered out. The default value is half of the populations [default ceiling(nPop(x)/2)].
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].
Custodian: Luis Mijangos -- Post to https://groups.google.com/d/forum/dartr
gl.report.ld.map
Other matched filter:
gl.filter.callrate(),
gl.filter.hamming(),
gl.filter.locmetric(),
gl.filter.maf(),
gl.filter.monomorphs(),
gl.filter.overshoot(),
gl.filter.pa(),
gl.filter.secondaries()