dartR (version 1.9.9.1)

gl.filter.heterozygosity: Filters individuals with average heterozygosity greater than a specified upper threshold or less than a specified lower threshold.

Description

Calculates the observed heterozyosity 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

Examples

# NOT RUN {
 result <- gl.filter.heterozygosity(testset.gl,t.upper=0.06,verbose=3)
 tmp <- gl.report.heterozygosity(result,method="ind")
# }