gl2gds: Converts a genlight object into gds format

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

Converts a genlight object into gds format

Description

Package SNPRelate relies on a bit-level representation of a SNP dataset that competes with {adegenet} genlight objects and associated files. This function converts a genlight object to a gds format file.

Usage

gl2gds(
  x,
  outfile = "gl_gds.gds",
  outpath = tempdir(),
  snp_pos = "0",
  snp_chr = "0",
  chr_format = "character",
  verbose = NULL
)

Arguments

x	Name of the genlight object containing the SNP data [required].
outfile	File name of the output file (including extension) [default 'gl_gds.gds'].
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.
snp_pos	Field name from the slot loc.metrics where the SNP position is stored [default '0'].
snp_chr	Field name from the slot loc.metrics where the chromosome of each is stored [default '0'].
chr_format	Whether chromosome information is stored as 'numeric' or as 'character', see details [default 'character'].
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

This function orders the SNPS by chromosome and by position before converting to SNPRelate format, as required by this package.

The chromosome of each SNP can be a character or numeric, as described in the vignette of SNPRelate: 'snp.chromosome, an integer or character mapping for each chromosome. Integer: numeric values 1-26, mapped in order from 1-22, 23=X, 24=XY (the pseudoautosomal region), 25=Y, 26=M (the mitochondrial probes), and 0 for probes with unknown positions; it does not allow NA. Character: “X”, “XY”, “Y” and “M” can be used here, and a blank string indicating unknown position.'

When using some functions from package SNPRelate with datasets other than humans it might be necessary to use the option autosome.only=FALSE to avoid detecting chromosome coding. So, it is important to read the documentation of the function before using it.

The chromosome information for unmapped SNPS is coded as 0, as required by SNPRelate.

Remember to close the GDS file before working in a different GDS object with the function snpgdsClose (package SNPRelate).

Value

returns no value (i.e. NULL)

Author(s)

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

Examples

require("dartR.data")
gl2gds(platypus.gl,snp_pos='ChromPos_Platypus_Chrom_NCBIv1',
snp_chr = 'Chrom_Platypus_Chrom_NCBIv1')

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