gl.alf: Calculates allele frequency of the first and second allele...

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

Calculates allele frequency of the first and second allele for each locus A very simple function to report allele frequencies

Description

Calculates allele frequency of the first and second allele for each locus A very simple function to report allele frequencies

Usage

gl.alf(x)

Arguments

x	Name of the genlight object [required].

Value

A simple data.frame with ref (reference allele), alt (alternate allele).

Author(s)

Bernd Gruber (bugs? Post to https://groups.google.com/d/forum/dartr)

See Also

Other utilities: utils.check.datatype(), utils.collapse.matrix(), utils.dart2genlight(), utils.dist.binary(), utils.flag.start(), utils.hamming(), utils.het.pop(), utils.impute, utils.is.fixed(), utils.jackknife(), utils.n.var.invariant(), utils.plot.save(), utils.read.fasta(), utils.read.ped(), utils.recalc.avgpic(), utils.recalc.callrate(), utils.recalc.freqhets(), utils.recalc.freqhomref(), utils.recalc.freqhomsnp(), utils.recalc.maf(), utils.reset.flags(), utils.transpose(), utils.vcfr2genlight.polyploid()

Examples

#for the first 10 loci only
#Deprecated:
gl.alf(possums.gl[,1:10])
barplot(t(as.matrix(gl.alf(possums.gl[,1:10]))))
#Current:
gl.allele.freq(possums.gl[,1:10],simple=TRUE)
barplot(t(as.matrix(gl.allele.freq(possums.gl[,1:10],simple=TRUE))))

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