gl.filter.heterozygosity: Filters individuals with average heterozygosity greater than...

In green-striped-gecko/dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

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.pa(), gl.filter.parent.offspring(), 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')

green-striped-gecko/dartR documentation built on Sept. 7, 2024, 4:15 a.m.