| gl2genepop {dartR.base} | R Documentation |
Converts a genlight object into genepop format (and file)
Description
The genepop format is used by several external applications (for example Neestimator2 (http://www.molecularfisherieslaboratory.com.au/neestimator-software/). So the main idea is to create the genepop file and then run the other software externally. As a feature, the genepop file is also returned as an invisible data.frame by the function.
Usage
gl2genepop(
x,
outfile = "genepop.gen",
outpath = NULL,
pop.order = "alphabetic",
output.format = "2_digits",
verbose = NULL
)
Arguments
x |
Name of the genlight object containing the SNP data [required]. |
outfile |
File name of the output file [default 'genepop.gen']. |
outpath |
Path where to save the output file [default global working directory or if not specified, tempdir()]. |
pop.order |
Order of the output populations either "alphabetic" or a vector of population names in the order required by the user (see examples) [default "alphabetic"]. |
output.format |
Whether to use a 2-digit format ("2_digits") or 3-digits format ("3_digits") [default "2_digits"]. |
verbose |
Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default 2, unless specified using gl.set.verbosity]. |
Value
Invisible data frame in genepop format
Author(s)
Custodian: Bernd Gruber (Post to https://groups.google.com/d/forum/dartr)
See Also
Other linker:
gl2bayesAss(),
gl2bayescan(),
gl2bpp(),
gl2demerelate(),
gl2eigenstrat(),
gl2faststructure(),
gl2gds(),
gl2genalex(),
gl2geno(),
gl2gi(),
gl2hiphop(),
gl2phylip(),
gl2plink(),
gl2related(),
gl2sa(),
gl2structure(),
gl2treemix(),
gl2vcf()
Examples
require("dartR.data")
# SNP data
geno <- gl2genepop(possums.gl[1:3,1:9], outpath = tempdir())
head(geno)
test <- gl.filter.callrate(platypus.gl,threshold = 1)
popNames(test)
gl2genepop(test, pop.order = c("TENTERFIELD","SEVERN_ABOVE","SEVERN_BELOW"),
output.format="3_digits", outpath = tempdir())