GenotypeInfo

Create a genotype information object

Description

GenotypeInfo() creates a facade for genotype operations.

Usage

GenotypeInfo(
  name,
  path,
  files = NULL,
  files.pattern = ".*",
  format = c("vcf", "bfile", "pfile"),
  build,
  samples = NULL,
  logger = NULL,
  plink = NULL,
  nthreads = NULL,
  ...
)

Arguments

name	Character scalar. Name for the genotype information object.
path	Character scalar. Directory containing genotype files.
files	Character vector or NULL. For bfile and pfile, entries are fileset stems without extensions. For vcf, entries are full VCF filenames relative to path. When NULL, files are discovered with files.pattern.
files.pattern	Character scalar or NULL. Regular expression used to discover files when files is NULL.
format	Character scalar. One of “vcf”, “bfile”, or “pfile”.
build	Character scalar genome-build key or name understood by workspace$catalogs$genomeBuilds.
samples	Optional character vector of IIDs to include in the working set. When NULL, all discovered samples are included.
logger	Optional logger object.
plink	Optional character scalar path to the PLINK 2 executable. When NULL, the path is resolved from workspace$catalogs$plink.
nthreads	Optional positive integer PLINK thread count used during initialization for operations that require PLINK sample discovery.
…	Additional named values stored as public fields on the returned R6 object.

Value

An R6 object of class GenotypeInfo.