gl.filter.excess.het: Filters excessively-heterozygous loci from a genlight object

In dartR.base: Analysing 'SNP' and 'Silicodart' Data - Basic Functions

Filters excessively-heterozygous loci from a genlight object

Description

Calculates excess of heterozygosity in a genlight object and remove those loci

Usage

gl.filter.excess.het(
  x,
  Yates = FALSE,
  mono.rm = FALSE,
  recalc = FALSE,
  verbose = NULL
)

Arguments

x	A genlight object containing the SNP genotypes [required].
Yates	Whether to use Yates's continuity correction [default FALSE].
mono.rm	Remove monomorphic loci after analysis is complete [default FALSE].
recalc	Recalculate the locus metadata statistics if any individuals are deleted in the filtering [default FALSE].
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

Returns unaltered genlight object

Author(s)

Author(s): Jesús Castrejón-Figueroa, Diana A Robledo-Ruiz (Custodian: Ching Ching Lau) – Post to https://groups.google.com/d/forum/dartr

References

• https://github.com/drobledoruiz/conservation_genomics/tree/main/filter.excess.het

• Robledo‐Ruiz, D. A., Austin, L., Amos, J. N., Castrejón‐Figueroa, J., Harley, D. K., Magrath, M. J., Sunnucks, P. & Pavlova, A. (2023). Easy‐to‐use R functions to separate reduced‐representation genomic datasets into sex‐linked and autosomal loci, and conduct sex assignment. Molecular Ecology Resources.

See Also

gl.filter.callrate

Other matched report: gl.report.allna(), gl.report.callrate(), gl.report.hamming(), gl.report.locmetric(), gl.report.maf(), gl.report.overshoot(), gl.report.pa(), gl.report.rdepth(), gl.report.reproducibility(), gl.report.secondaries(), gl.report.taglength()

Examples

filtered.gl <- gl.filter.excess.het(x = LBP, Yates = TRUE)
# Use below function to output information of the loci with Yates's continuity correction specified 
filtered.table <- gl.report.excess.het(x = LBP, Yates = TRUE)

dartR.base documentation built on April 4, 2025, 2:45 a.m.