batchconvert: Convert all Genepop files in dir to Arlequin format

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.

Usage

batchconvert(ndigit = 3)

Arguments

ndigit

The number of digits per allele in the input file. Can be 2 or 3 (default 3).

Details

Relies on the function convert to perform the batch conversion.

Input files must end with the extension '.gen'. Make sure to follow standard Genepop format for input files. 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.

Value

All arp files and the single arb file are saved 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.

See Also

convert

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