gl.filter.heterozygosity {dartR.base}

Filters individuals with average heterozygosity greater than a specified upper threshold or less than a specified lower threshold @family matched filter

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

Examples

 result <- gl.filter.heterozygosity(testset.gl,t.upper=0.06,verbose=3)
 tmp <- gl.report.heterozygosity(result,method='ind')