subset_filebacked {plmmr}R Documentation

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:


[Package plmmr version 4.1.0 Index]