read_plink_files: A function to read in PLINK files using 'bigsnpr' methods

In plmmr: Penalized Linear Mixed Models for Correlated Data

A function to read in PLINK files using bigsnpr methods

Description

A function to read in PLINK files using bigsnpr methods

Usage

read_plink_files(
  data_dir,
  data_prefix,
  rds_dir,
  outfile,
  parallel,
  overwrite,
  quiet
)

Arguments

data_dir	The path to the bed/bim/fam data files, without a trailing "/" (e.g., use data_dir = '~/my_dir', not data_dir = '~/my_dir/')
data_prefix	The prefix (as a character string) of the bed/fam data files (e.g., prefix = 'mydata')
rds_dir	The path to the directory in which you want to create the new '.rds' and '.bk' files. Defaults to data_dir
outfile	Optional: the name (character string) of the prefix of the logfile to be written. Defaults to 'process_plink', i.e. you will get 'process_plink.log' as the outfile.
parallel	Logical: should the computations within this function be run in parallel? Defaults to TRUE. See count_cores() and ?bigparallelr::assert_cores for more details. In particular, the user should be aware that too much parallelization can make computations slower.
overwrite	Logical: if existing .bk/.rds files exist for the specified directory/prefix, should these be overwritten? Defaults to FALSE. Set to TRUE if you want to change the imputation method you're using, etc.
quiet	Logical: should messages be printed to the console? Defaults to TRUE

Value

'.rds' and '.bk' files are created in data_dir, and obj (a bigSNP object) is returned. See bigsnpr documentation for more info on the bigSNP class.

plmmr documentation built on April 4, 2025, 12:19 a.m.