gl2geno: Converts a genlight object to geno format from package LEA

In dartR.base: Analysing 'SNP' and 'Silicodart' Data - Basic Functions

Converts a genlight object to geno format from package LEA

Description

The function converts a genlight object (SNP or presence/absence i.e. SilicoDArT data) into a file in the 'geno' and the 'lfmm' formats from (package LEA).

The function converts a genlight object (SNP or presence/absence i.e. SilicoDArT data) into a file in the 'geno' and the 'lfmm' formats from (package LEA).

Usage

gl2gapit(x, outfile = "gl_gapit", outpath = NULL, verbose = NULL)

gl2geno(x, outfile = "gl_geno", outpath = NULL, verbose = NULL)

Arguments

x	Name of the genlight object containing the SNP or presence/absence (SilicoDArT) data [required].
outfile	File name of the output file [default 'gl_geno'].
outpath	Path where to save the output file [default global working directory or if not specified, tempdir()].
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

returns no value (i.e. NULL)

returns no value (i.e. NULL)

Author(s)

Custodian: Luis Mijangos (Post to https://groups.google.com/d/forum/dartr)

See Also

Other linker: gl2bayesAss(), gl2bayescan(), gl2bpp(), gl2demerelate(), gl2eigenstrat(), gl2faststructure(), gl2gds(), gl2genalex(), gl2genepop(), gl2gi(), gl2hiphop(), gl2phylip(), gl2plink(), gl2related(), gl2sa(), gl2structure(), gl2treemix(), gl2vcf()

Other linker: gl2bayesAss(), gl2bayescan(), gl2bpp(), gl2demerelate(), gl2eigenstrat(), gl2faststructure(), gl2gds(), gl2genalex(), gl2genepop(), gl2gi(), gl2hiphop(), gl2phylip(), gl2plink(), gl2related(), gl2sa(), gl2structure(), gl2treemix(), gl2vcf()

Examples

# SNP data
t1 <- platypus.gl
# assigning chromosomet1
t1$chromosome <- t1$other$loc.metrics$Chrom_Platypus_Chrom_NCBIv1
# assigning SNP position
t1$position <- t1$other$loc.metrics$ChromPos_Platypus_Chrom_NCBIv1
res <- gl2gapit(t1)

# SNP data
gl2geno(testset.gl, outpath=tempdir())
# Tag P/A data
gl2geno(testset.gs, outpath=tempdir())

dartR.base documentation built on April 4, 2025, 2:45 a.m.