standardize_filebacked: A helper function to standardize a filebacked matrix

In plmmr: Penalized Linear Mixed Models for Correlated Data

A helper function to standardize a filebacked matrix

Description

A helper function to standardize a filebacked matrix

Usage

standardize_filebacked(
  X,
  new_file,
  rds_dir,
  non_gen,
  complete_outcome,
  id_var,
  outfile,
  quiet,
  overwrite
)

Arguments

X	A list that includes: (1) subset_X: a big.matrix object that has been subset &/or had any additional predictors appended as columns (2) ns: a numeric vector indicating the indices of nonsingular columns in subset_X
new_file	The new_file (as a character string) of the bed/fam data files (e.g., new_file = '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 new_file of the logfile to be written. Defaults to 'process_plink', i.e. you will get 'process_plink.log' as the outfile.
quiet	Logical: should messages be printed to the console? Defaults to FALSE (which leaves the print messages on...)
overwrite	Logical: if existing .bk/.rds files exist for the specified directory/new_file, should these be overwritten?

Value

A list with a new component of obj called 'std_X' - this is an FBM with column-standardized data. List also includes several other indices/meta-data on the standardized matrix

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