dartR: gl.write.csv – R documentation

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gl.write.csv

Write out data from a gl object adegenet to csv file

Description

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.

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]

Details

The data coding differs from the DArT 1row format in that 0 = reference homozygous, 2 = alternate homozygous, 1 = heterozyous, and NA = missing SNP assignment.

Value

saves a glenlight object to csv, returns NULL

Author(s)

Arthur Georges (Post to https://groups.google.com/d/forum/dartr)

Examples

# SNP data
  gl.write.csv(testset.gl, outfile="SNP_1row.csv")
# Tag P/A data
  gl.write.csv(testset.gs, outfile="PA_1row.csv")

dartR

Importing and Analysing SNP and Silicodart Data Generated by Genome-Wide Restriction Fragment Analysis

v1.9.6

GPL-2

Authors

Bernd Gruber [aut, cre], Arthur Georges [aut], Jose L. Mijangos [aut], Peter J. Unmack [ctb], Oliver Berry [ctb], Lindsay V. Clark [ctb], Floriaan Devloo-Delva [ctb]

Initial release

2021-04-29