freq.to.genpop: Convert Allele Frequencies for Adegenet
In polysat: Tools for Polyploid Microsatellite Analysis

freq.to.genpop

R Documentation

Convert Allele Frequencies for Adegenet

Description

Given a data frame of allele frequencies such as that produced by simpleFreq or deSilvaFreq, freq.to.genpop creates a data frame of allele counts that can be read by the as.genpop function in the package adegenet.

Usage

freq.to.genpop(freqs, pops = row.names(freqs),
               loci =
                unique(as.matrix(as.data.frame(strsplit(names(freqs),
                split = ".", fixed = TRUE), stringsAsFactors = FALSE))[1, ]))

Arguments

`freqs`	A data frame of allele frequencies. Row names are population names. The first column is called `"Genomes"` and indicates the size of each population in terms of number of haploid genomes. All other column names are the locus and allele separated by a period. These columns contain the frequencies of each allele in each population. For each locus and population, all frequencies should total to 1.
`pops`	An optional character vector indicating the names of populations to use.
`loci`	An optional character vector indicating the names of loci to use.

Details

adegenet expects one ploidy for the entire dataset. Therefore, data frames of allele frequencies with multiple “Genomes” columns, such as those produced when ploidy varies by locus, are not allowed as the freqs argument.

Value

A data frame with row and column names identical to those in freqs, minus the "Genomes" column and any columns for loci not included in loci. Allele frequencies are converted to counts by multiplying by the values in the "Genomes" column and rounding to the nearest integer.

Author(s)

Lindsay V. Clark

References

Jombart, T. (2008) adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24, 1403-1405.

Examples

# create a simple allele frequency table
# (usually done with simpleFreq or deSilvaFreq)
myfreq <- data.frame(row.names=c("popA","popB"), Genomes=c(120,100),
                     locG.152=c(0.1,0.4), locG.156=c(0.5, 0.3),
                     locG.160=c(0.4, 0.3), locK.179=c(0.15, 0.25),
                     locK.181=c(0.35, 0.6), locK.183=c(0.5, 0.15))
myfreq

# convert to adegenet format
gpfreq <- freq.to.genpop(myfreq)
gpfreq

## Not run: 
# If you have adegenet installed, you can now make this into a
# genpop object.
require(adegenet)
mygenpop <- genpop(gpfreq, ploidy=as.integer(4), type="codom")

# examine the object that has been created
mygenpop
popNames(mygenpop)
mygenpop@tab
mygenpop@all.names

# Perform a distance calculation with the object
dist.genpop(mygenpop)

## End(Not run)

polysat documentation built on Aug. 23, 2022, 5:07 p.m.