dartR: gl.filter.heterozygosity – R documentation

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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

Author(s)

Arthur Georges (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")

dartR

Importing and Analysing SNP and Silicodart Data Generated by Genome-Wide Restriction Fragment Analysis

v1.9.6

GPL-2

Authors

Bernd Gruber [aut, cre], Arthur Georges [aut], Jose L. Mijangos [aut], Peter J. Unmack [ctb], Oliver Berry [ctb], Lindsay V. Clark [ctb], Floriaan Devloo-Delva [ctb]

Initial release

2021-04-29