Converts a genlight object into a format suitable for input to genalex
Source:R/gl2genalex.r
gl2genalex.Rd
The output csv file contains the snp data and other relevant lines suitable for genalex. This script is a wrapper for genind2genalex (package poppr).
Usage
gl2genalex(
x,
outfile = "genalex.csv",
outpath = tempdir(),
overwrite = FALSE,
verbose = NULL
)
Arguments
- x
Name of the genlight object containing the SNP data [required].
- outfile
File name of the output file (including extension) [default 'genalex.csv'].
- outpath
Path where to save the output file [default tempdir()].
- overwrite
If FALSE and filename exists, then the file will not be overwritten. Set this option to TRUE to overwrite the file [default FALSE].
- verbose
Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default 2 or as specified using gl.set.verbosity].
References
Peakall, R. and Smouse P.E. (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics 28, 2537-2539. http://bioinformatics.oxfordjournals.org/content/28/19/2537
Author
Custodian: Luis Mijangos, Author: Katrin Hohwieler, wrapper Arthur Georges (Post to https://groups.google.com/d/forum/dartr)