| gl.filter.heterozygosity {dartR} | R Documentation |
Filters individuals with average heterozygosity greater than a specified upper threshold or less than a specified lower threshold
Description
Calculates the observed heterozygosity for each individual in a genlight object and filters individuals based on specified threshold values. Use gl.report.heterozygosity to determine the appropriate thresholds.
Usage
gl.filter.heterozygosity(x, t.upper = 0.7, t.lower = 0, verbose = NULL)
Arguments
x |
A genlight object containing the SNP genotypes [required]. |
t.upper |
Filter individuals > the threshold [default 0.7]. |
t.lower |
Filter individuals < the threshold [default 0]. |
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]. |
Value
The filtered genlight object.
Author(s)
Custodian: Luis Mijangos – Post to https://groups.google.com/d/forum/dartr
See Also
Other filter functions:
gl.filter.allna(),
gl.filter.callrate(),
gl.filter.hwe(),
gl.filter.ld(),
gl.filter.locmetric(),
gl.filter.maf(),
gl.filter.monomorphs(),
gl.filter.overshoot(),
gl.filter.parent.offspring(),
gl.filter.pa(),
gl.filter.rdepth(),
gl.filter.reproducibility(),
gl.filter.secondaries(),
gl.filter.sexlinked(),
gl.filter.taglength()
Examples
result <- gl.filter.heterozygosity(testset.gl,t.upper=0.06,verbose=3)
tmp <- gl.report.heterozygosity(result,method='ind')