vcf2pcadapt: vcfR-based converter
Description
vcf2pcadapt uses the package vcfR to extract the genotype information from a vcf file and exports it
under the format required by pcadapt.
Usage
vcf2pcadapt(geno, output.file = "tmp.pcadapt", allele.sep = "/", blocksize = 10000, console.count = 10000)
Arguments
geno
a genotype matrix obtained with `vcfR`.
output.file
a character string indicating the name of the output file.
allele.sep
a character indicating which type of delimiter is used to separate the alleles.
blocksize
an integer indicating the number of SNPs to be processed in the same chunk.
console.count
an integer indicating the number of SNPs by which the progress bar should increment.
Examples
Run this code## see also ?pcadapt for examples
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