gl.write.csv: Writes out data from a genlight object to csv file

In green-striped-gecko/dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

Writes out data from a genlight object 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.

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].

Value

Saves a genlight object to csv, returns NULL.

Author(s)

Custodian: 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')

green-striped-gecko/dartR documentation built on Jan. 31, 2024, 10:14 a.m.