dartR (version 1.9.9.1)

gl.report.maf: Report minor allele frequency (MAF) for each locus in a SNP dataset

Description

This script provides summary histograms of MAF for each population in the dataset as a basis for decisions on filtering.

Usage

gl.report.maf(
  x,
  maf.limit = 0.5,
  ind.limit = 5,
  loc.limit = 30,
  verbose = NULL
)

Arguments

x

-- name of the genlight object containing the SNP data [required]

maf.limit

-- show histograms maf range <= maf.limit [default 0.5]

ind.limit

-- show histograms only for populations of size greater than ind.limit [default 5]

loc.limit

-- show histograms only for populations with more than loc.limit polymorphic loci [default 30]

verbose

-- verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log ; 3, progress and results summary; 5, full report [default 2 or as specified using gl.set.verbosity]

Examples

# NOT RUN {
gl.report.maf(testset.gl)

# }