freqPCA: Create a table of allele frequencies from Arlequin file...

In PopGenKit: Useful functions for (batch) file conversion and data resampling in microsatellite datasets

Description

This function will take a Arlequin input file (.arp) of multilocus genotypes and create a table of allele frequencies for multivariate analyses. For each locus, one allele is omitted, as it would be a redundant character for PCA analyses.

Usage

freqPCA(datafile, ndigit = 3, default.pop = T, vecpops)

Arguments

datafile	Name of the input Arlequin file, with extension (e.g. 'glyptemys3.arp').
ndigit	Number of digits per allele in input file. Can be 2 or 3. (Default is 3).
default.pop	If TRUE, population names will be taken from input file. If FALSE, they will be taken from an additional vector of population names. (Default is TRUE).
vecpops	Optional vector of population names, needed if default.pop is set to FALSE.

Details

Some .arp files might not be imported correctly depending on which software was used to generate them. If this is the case, start from the Genepop file and convert it first with convert.

Value

Returns a table of allele frequencies formatted for PCA analysis. Also saves the table in a file placed in the working directory.

Author(s)

Sebastien Rioux Paquette

References

Excoffier, L. and H.E.L. Lischer (2010). Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Mol. Ecol. Res. 10: 564-567.

Rousset, F. (2008). Genepop'007: a complete reimplementation of the Genepop software for Windows and Linux. Mol. Ecol. Res. 8: 103-106.

PopGenKit documentation built on May 2, 2019, 3:33 p.m.