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Extract variants from bulk data and load to memory

Source: R/extract_variants.R
extract_variants.Rd

Use user-provided list of genetic variants to extract from imputed BGEN files (field 22828) or WGS DRAGEN BGEN files (field 24309) data and load as data.frame

If selecting the DRAGEN data as the source, this assumes your project has access to the WGS BGEN files released April 2025. If not, run `ukbrapR:::make_dragen_bed_from_pvcfs()` to use [tabix] and [plink] to subset the [DRAGEN WGS pVCF files].

Usage

extract_variants(
  in_file,
  out_bed = "tmp",
  source = "imputed",
  overwrite = FALSE,
  progress = FALSE,
  verbose = FALSE,
  very_verbose = FALSE
)

Arguments

in_file

A data frame or file path. Contains rsid, chr, and pos. For imputed genos pos is build 37. For DRAGEN pos is build 38. Other columns are ignored.

out_bed

A string. Prefix for output files (optional) default="tmp"

source

A string. Either "imputed" or "dragen" - indicating whether the variants should be from "UKB imputation from genotype" (field 22828) or "DRAGEN population level WGS variants, PLINK format [500k release]" (field 24308) default="imputed"

overwrite

Logical. Overwrite output BED files? (If output prefix is left as 'tmp' overwrite is set to TRUE), default=FALSE

progress

Logical. Show progress through each individual file, default=FALSE

verbose

Logical. Be verbose (show individual steps), default=FALSE

very_verbose

Logical. Be very verbose (show individual steps & show terminal output from Plink etc), default=FALSE

Value

A data frame

Author

Luke Pilling

Examples


liver_variants <- extract_variants(in_file=system.file("files", "pgs_liver_cirrhosis.txt", package="ukbrapR"), out_bed="liver_cirrhosis.imputed.variants")