This function exports a genlight object into VCF format and save it into a file.
gl2vcf(
x,
plink_path = getwd(),
outfile = "gl_vcf",
outpath = tempdir(),
snp_pos = "0",
snp_chr = "0",
chr_format = "character",
pos_cM = "0",
ID_dad = "0",
ID_mom = "0",
sex_code = "unknown",
phen_value = "0",
verbose = NULL
)Name of the genlight object containing the SNP data [required].
Path of PLINK binary file [default getwd())].
File name of the output file [default 'gl_vcf'].
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.
Field name from the slot loc.metrics where the SNP position is stored [default '0'].
Field name from the slot loc.metrics where the chromosome of each is stored [default '0'].
Whether chromosome information is stored as 'numeric' or as 'character', see details [default 'character'].
A vector, with as many elements as there are loci, containing the SNP position in morgans or centimorgans [default '0'].
A vector, with as many elements as there are individuals, containing the ID of the father, '0' if father isn't in dataset [default '0'].
A vector, with as many elements as there are individuals, containing the ID of the mother, '0' if mother isn't in dataset [default '0'].
A vector, with as many elements as there are individuals, containing the sex code ('male', 'female', 'unknown') [default 'unknown'].
A vector, with as many elements as there are individuals, containing the phenotype value. '1' = control, '2' = case, '0' = unknown [default '0'].
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].
This function requires to download the binary file of PLINK 1.9 and provide its path (plink_path). The binary file can be downloaded from: https://www.cog-genomics.org/plink/
The chromosome information for unmapped SNPS is coded as 0. Family ID is taken from x$pop Within-family ID (cannot be '0') is taken from indNames(x) Variant identifier is taken from locNames(x)
Danecek, P., Auton, A., Abecasis, G., Albers, C. A., Banks, E., DePristo, M. A., ... & 1000 Genomes Project Analysis Group. (2011). The variant call format and VCFtools. Bioinformatics, 27(15), 2156-2158.
# NOT RUN {
gl2vcf(platypus.gl,snp_pos='ChromPos_Platypus_Chrom_NCBIv1',
snp_chr = 'Chrom_Platypus_Chrom_NCBIv1')
# }
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