This script writes to file the SNP genotypes with specimens as entities (columns) and loci as attributes (rows). Each row has associated locus metadata. Each column, with header of specimen id, has population in the first row.
The data coding differs from the DArT 1row format in that 0 = reference homozygous, 2 = alternate homozygous, 1 = heterozygous, and NA = missing SNP assignment.
Usage
gl.write.csv(x, outfile = "outfile.csv", outpath = tempdir(), verbose = NULL)Arguments
- x
Name of the genlight object containing the SNP data [required].
- outfile
File name of the output file (including extension) [default "outfile.csv"].
- outpath
Path where to save the output file [default tempdir(), mandated by CRAN]. Use outpath=getwd() or outpath='.' when calling this function to direct output files to your working directory.
- 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].
Author
Custodian: Arthur Georges – Post to https://groups.google.com/d/forum/dartr
Examples
# SNP data
gl.write.csv(testset.gl, outfile='SNP_1row.csv')
#> Starting gl.write.csv
#> Processing genlight object with SNP data
#> Writing records to /tmp/RtmpWgoHDI/SNP_1row.csv
#> Completed: gl.write.csv
#>
#> NULL
# Tag P/A data
gl.write.csv(testset.gs, outfile='PA_1row.csv')
#> Starting gl.write.csv
#> Processing genlight object with Presence/Absence (SilicoDArT) data
#> Writing records to /tmp/RtmpWgoHDI/PA_1row.csv
#> Completed: gl.write.csv
#>
#> NULL