subset_filebacked: A helper function to subset 'big.matrix' objects

In plmmr: Penalized Linear Mixed Models for Correlated Data

A helper function to subset big.matrix objects

Description

A helper function to subset big.matrix objects

Usage

subset_filebacked(X, new_file, complete_samples, ns, rds_dir, outfile, quiet)

Arguments

X	A filebacked big.matrix with the to-be-standardized design matrix
new_file	Optional user-specified new_file for the to-be-created .rds/.bk files.
complete_samples	Numeric vector with indicesmarking the rows of the original data which have a non-missing entry in the 6th column of the .fam file
ns	Numeric vector with the indices of the non-singular columns This vector is created in handle_missingness()
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...)

Value

A list with two components. First, a big.matrix object, 'subset_X', representing a design matrix wherein:

• rows are subset according to user's specification in handle_missing_phen

• columns are subset so that no constant features remain – this is important for standardization downstream The list also includes the integer vector 'ns' which marks which columns of the original matrix were 'non-singular' (i.e. not constant features). The 'ns' index plays an important role in plmm_format() and untransform() (both helper functions in model fitting)

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