gl2eigenstrat: Converts a genlight object into eigenstrat 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 eigenstrat format

Description

The output of this function are three files:

• genotype file: contains genotype data for each individual at each SNP with an extension 'eigenstratgeno.'

• snp file: contains information about each SNP with an extension 'snp.'

• indiv file: contains information about each individual with an extension 'ind.'

Usage

gl2eigenstrat(
  x,
  outfile = "gl_eigenstrat",
  outpath = tempdir(),
  snp_pos = 1,
  snp_chr = 1,
  pos_cM = 0,
  sex_code = "unknown",
  phen_value = "Case",
  verbose = NULL
)

Arguments

x	Name of the genlight object containing the SNP data [required].
outfile	File name of the output file [default 'gl_eigenstrat'].
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 1].
snp_chr	Field name from the slot loc.metrics where the chromosome of each is stored [default 1].
pos_cM	A vector, with as many elements as there are loci, containing the SNP position in morgans or centimorgans [default 1].
sex_code	A vector, with as many elements as there are individuals, containing the sex code ('male', 'female', 'unknown') [default 'unknown'].
phen_value	A vector, with as many elements as there are individuals, containing the phenotype value ('Case', 'Control') [default 'Case'].
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

Eigenstrat only accepts chromosomes coded as numeric values, as follows: X chromosome is encoded as 23, Y is encoded as 24, mtDNA is encoded as 90, and XY is encoded as 91. SNPs with illegal chromosome values, such as 0, will be removed.

Value

returns no value (i.e. NULL)

Author(s)

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

References

• Patterson, N., Price, A. L., & Reich, D. (2006). Population structure and eigenanalysis. PLoS genetics, 2(12), e190.

• Price, A. L., Patterson, N. J., Plenge, R. M., Weinblatt, M. E., Shadick, N. A., & Reich, D. (2006). Principal components analysis corrects for stratification in genome-wide association studies. Nature genetics, 38(8), 904-909.

Examples

require("dartR.data")
gl2eigenstrat(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.