gl.alf: Calculates allele frequency of the first and second allele...
| gl.alf | R Documentation |
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))))
