create_design_filebacked: A function to create a design matrix, outcome, and penalty...

In plmmr: Penalized Linear Mixed Models for Correlated Data

A function to create a design matrix, outcome, and penalty factor to be passed to a model fitting function

Description

A function to create a design matrix, outcome, and penalty factor to be passed to a model fitting function

Usage

create_design_filebacked(
  data_file,
  rds_dir,
  obj,
  new_file,
  feature_id = NULL,
  add_outcome,
  outcome_id,
  outcome_col,
  na_outcome_vals = c(-9, NA_integer_),
  add_predictor = NULL,
  predictor_id = NULL,
  unpen = NULL,
  logfile = NULL,
  overwrite = FALSE,
  quiet = FALSE
)

Arguments

data_file	A filepath to rds file of processed data (data from process_plink() or process_delim())
rds_dir	The path to the directory in which you want to create the new '.rds' and '.bk' files.
obj	The RDS object read in by create_design()
new_file	User-specified filename (without .bk/.rds extension) for the to-be-created .rds/.bk files. Must be different from any existing .rds/.bk files in the same folder.
feature_id	A string specifying the column in the data X (the feature data) with the row IDs (e.g., identifiers for each row/sample/participant/, etc.). No duplicates allowed. - for PLINK data: a string specifying an ID column of the PLINK .fam file. Options are "IID" (default) and "FID" - for all other filebacked data: a character vector of unique identifiers (IDs) for each row of the feature data (i.e., the data processed with process_delim()) - if left NULL (default), X is assumed to have the same row-order as add_outcome. Note: if this assumption is made in error, calculations downstream will be incorrect. Pay close attention here.
add_outcome	A data frame or matrix with two columns: and ID column and a column with the outcome value (to be used as 'y' in the final design). IDs must be characters, outcome must be numeric.
outcome_id	A string specifying the name of the ID column in 'add_outcome'
outcome_col	A string specifying the name of the phenotype column in 'add_outcome'
na_outcome_vals	A vector of numeric values used to code NA values in the outcome. Defaults to c(-9, NA_integer) (the -9 matches PLINK conventions).
add_predictor	Optional (for PLINK data only): a matrix or data frame to be used for adding additional unpenalized covariates/predictors/features from an external file (i.e., not a PLINK file). This matrix must have one column that is an ID column; all other columns aside the ID will be used as covariates in the design matrix. Columns must be named.
predictor_id	Optional (for PLINK data only): A string specifying the name of the column in 'add_predictor' with sample IDs. Required if 'add_predictor' is supplied. The names will be used to subset and align this external covariate with the supplied PLINK data.
unpen	Optional (for delimited file data only): an optional character vector with the names of columns to mark as unpenalized (i.e., these features would always be included in a model). Note: if you choose to use this option, X must have column names.
logfile	Optional: name of the '.log' file to be written – Note: do not append a .log to the filename; this is done automatically.
overwrite	Logical: should existing .rds files be overwritten? Defaults to FALSE.
quiet	Logical: should messages to be printed to the console be silenced? Defaults to FALSE

Value

A filepath to the created .rds file containing all the information for model fitting, including a standardized X and model design information

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