read_data_files: A function to read in a large file as a numeric file-backed...

In plmmr: Penalized Linear Mixed Models for Correlated Data

A function to read in a large file as a numeric file-backed matrix (FBM) Note: this function is a wrapper for bigstatsr::big_read()

Description

A function to read in a large file as a numeric file-backed matrix (FBM) Note: this function is a wrapper for bigstatsr::big_read()

Usage

read_data_files(
  data_file,
  data_dir,
  rds_dir,
  rds_prefix,
  outfile,
  overwrite,
  quiet,
  ...
)

Arguments

data_file	The name of the file to read, not including its directory. Directory should be specified in data_dir
data_dir	The path to the directory where 'file' is
rds_dir	The path to the directory in which you want to create the new '.rds' and '.bk' files. Defaults to data_dir
rds_prefix	String specifying the user's preferred filename for the to-be-created .rds/.bk files (will be create insie rds_dir folder) Note: 'rds_prefix' cannot be the same as 'data_file'
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.
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
...	Optional: other arguments to be passed to bigmemory::read.big.matrix(). Note: 'sep' is an option to pass here.

Value

'.rds', '.bk', and '.desc' files are created in data_dir, and obj (a filebacked ⁠bigmemory big.matrix⁠ object) is returned. See bigmemory documentation for more info on the big.matrix class.

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