batchconvertjack: Convert all Genepop files in dir to Arlequin format while...

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

Description

This function converts all Genepop files (extension .gen) in the working directory to Arlequin files (extension .arp). It also creates a batch Arlequin file (extension .arb) to allow batch analysis in Arlequin. The user specifies a subset of loci to be removed.

Usage

batchconvertjack(ndigit = 3, rm.loci)

Arguments

ndigit	The number of digits per allele in the input file. Can be 2 or 3 (default is 3).
rm.loci	A vector indicating which locus or loci to remove from the final output file. Loci should be indicated as numbers according to the order in which they are listed in the input file (e.g. c(1,3) would remove the first and third loci).

Details

Relies on the function convertjack to do file conversion.

Input file must end with the extension '.gen'. Make sure to follow standard Genepop format for input file. The IDs of all individuals should be immediately followed by a comma. Population labels should be Pop, POP, or pop. There should not be invisible characters (tabs or spaces) at the end of lines, especially lines on which population labels are found. These lines should have only three characters (Pop). See example file 'glyptemys3.gen' if needed.

The option to remove loci from the output files can be extremely useful in simulation studies, in order to assess the influence of certain markers or estimate confidence intervals with jackkniffing procedures. Among others, Easypop generates Genepop files that could be processed with this function.

Value

All arp files and the single arb file are saved in the working directory

Author(s)

Sebastien Rioux Paquette

References

Balloux, F. (2001). EASYPOP (version 1.7): A computer program for population genetics simulations. J. Hered. 92: 301–302.

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.