Converts a VCFArrow object to a PLINK .bed format infile plus ADMIXTURE-specific .pop file
Usage
vcf2admixture(
vcf_arrow,
out_file,
keep_groups = NULL,
sex = NULL,
pheno = NULL,
chrom_code = c("zero", "auto", "index", "keep"),
supervised = FALSE,
reference_groups = NULL
)Arguments
- vcf_arrow
-> VCFArrow object
- out_file
-> output file prefix; extensions are added automatically, no default (character)
- keep_groups
-> groups to retain, default NULL (character)
- sex
-> vector of sexes of samples, default NULL (character)
- pheno
-> vector of phenotypes of samples, default NULL (character)
- chrom_code
-> how CHROM is written: "auto" (keep numeric CHROM, otherwise 0), "index" (1..n by first appearance), "zero" (all 0) or "keep" (verbatim), default "zero" (character)
- supervised
-> flag to generate .pop for use in ADMIXTURE's supervised mode, default FALSE (Boolean)
- reference_groups
-> vector of ancestry group labels, default NULL (character)
Details
This function converts a VCFArrow object to an external PLINK .bed formatted file. Writing occurs in chunks whose size is determined by the read_vcf() function. Larger chunks result in faster writing speeds. If no groups are defined, the default behavior is to use all groups. Sex and phenotype vectors are optional. If not defined sex = 0, pheno = -9. For supervised analyses, the supervised flag needs to be true to generate .pop file needed for ADMIXTURE's supervised mode. The reference_groups vector specifies ancestral information of individuals. When NULL, or for any missing individual, ancestry is inferred.
Examples
f <- system.file("extdata", "vaillantii_discosnp_sub.vcf.gz",
package = "VCFArrow")
vcf <- read_vcf(f) |> set_vcf_groups(dirname(f))
#> ℹ VCF is being read in chunks of 50000 variants
#> ✔ VCF successfully read into a VCFArrow object
vcf2admixture(vcf, out_file = file.path(tempdir(), "admixture_in"))
#> ℹ Building PLINK: 9313 variants x 18 samples (0 MiB raw storage)
#> ℹ Writing PLINK files...
#> ℹ Chromosome names were recoded as integers for PLINK compatibility; mapping written to /tmp/RtmpSpcr9J/admixture_in.chrommap
#> ✔ PLINK binary fileset written to /tmp/RtmpSpcr9J/admixture_in.bed, /tmp/RtmpSpcr9J/admixture_in.bim, /tmp/RtmpSpcr9J/admixture_in.fam
vcf2admixture(vcf, out_file = file.path(tempdir(), "admixture_sup"),
supervised = TRUE,
reference_groups = c("GS", "BS", "WA"))
#> ℹ Building PLINK: 9313 variants x 18 samples (0 MiB raw storage)
#> ℹ Writing PLINK files...
#> ℹ Chromosome names were recoded as integers for PLINK compatibility; mapping written to /tmp/RtmpSpcr9J/admixture_sup.chrommap
#> ✔ PLINK binary fileset written to /tmp/RtmpSpcr9J/admixture_sup.bed, /tmp/RtmpSpcr9J/admixture_sup.bim, /tmp/RtmpSpcr9J/admixture_sup.fam
#> ✔ ADMIXTURE .pop file written to /tmp/RtmpSpcr9J/admixture_sup.pop
#> ℹ Supervised mode: 15 reference samples, 3 samples with ancestry to be estimated.