gl2sa {dartR.base}

Converts genlight objects to the format used in the SNPassoc package

Description

This function exports a genlight object into a SNPassoc object. See package SNPassoc for details. This function needs package SNPassoc. At the time of writing (August 2020) the package was no longer available from CRAN. To install the package check their github repository. https://github.com/isglobal-brge/SNPassoc and/or use install_github('isglobal-brge/SNPassoc') to install the function and uncomment the function code.

Usage

gl2sa(x, installed = FALSE, verbose = NULL)

Arguments

x

Name of the genlight object containing the SNP data [required].

installed

Switch to run the function once SNPassoc package i s installed [default FALSE].#' @param 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].

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].

Value

Returns an object of class 'snp' to be used with SNPassoc.

Author(s)

Bernd Guber (Post to https://groups.google.com/d/forum/dartr)

References

Gonzalez, J.R., Armengol, L., Sol?, X., Guin?, E., Mercader, J.M., Estivill, X. and Moreno, V. (2017). SNPassoc: an R package to perform whole genome association studies. Bioinformatics 23:654-655.

See Also

Other linker: gl2bayesAss(), gl2bayescan(), gl2bpp(), gl2demerelate(), gl2eigenstrat(), gl2faststructure(), gl2gds(), gl2genalex(), gl2genepop(), gl2geno(), gl2gi(), gl2hiphop(), gl2phylip(), gl2plink(), gl2related(), gl2structure(), gl2treemix(), gl2vcf()