read_plink2_pgen_file_from_files: Read a 'PLINK2' '.pgen' file using a '.psam' and '.pvar'...
In richelbilderbeek/plinkr: Interface to PLINK

View source: R/read_plink2_pgen_file_from_files.R

read_plink2_pgen_file_from_files

R Documentation

Read a `PLINK2` `.pgen` file using a `.psam` and `.pvar` file.

Description

Read a PLINK2 .pgen file using a .psam and .pvar file. These two accessory files are used to extract the names of the individuals and the names of the loci. Use read_plink2_pgen_file to read a .pgen file without those two accessory files.

Usage

read_plink2_pgen_file_from_files(
  pgen_filename,
  psam_filename,
  pvar_filename,
  verbose = FALSE
)

Arguments

`pgen_filename`	name of a `PLINK2` `.pgen` file Use read_plink2_pgen_file to read a `PLINK2` `.pgen` file
`psam_filename`	name of a `PLINK2` `.psam` file Use read_plink2_psam_file to read a `PLINK2` `.psam` file
`pvar_filename`	name of a `PLINK2` `.pvar` file Use read_plink2_pvar_file to read a `PLINK2` `.pvar` file
`verbose`	the verbosity of a function. Set to TRUE for more output. Use check_verbose to detect if this argument is valid.

Author(s)

Richèl J.C. Bilderbeek

Examples

read_plink2_pgen_file_from_files(
  pgen_filename = get_plinkr_filename(
    "toy_v1_9_after_make-bed_after_make-pgen.pgen"
  ),
  psam_filename = get_plinkr_filename(
    "toy_v1_9_after_make-bed_after_make-pgen.psam"
  ),
  pvar_filename = get_plinkr_filename(
    "toy_v1_9_after_make-bed_after_make-pgen.pvar"
  )
)

richelbilderbeek/plinkr documentation built on March 25, 2024, 3:18 p.m.