dartR: gl.report.maf – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

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]

Author(s)

Arthur Georges (Post to https://groups.google.com/d/forum/dartr)

Examples

gl.report.maf(testset.gl)

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