plmmr (version 4.2.3)

untransform: Untransform coefficient values back to the original scale

Description

This function unwinds the initial standardization of the data to obtain coefficient values on their original scale. It is called by plmm_format().

Usage

untransform(
  std_scale_beta,
  p,
  std_X_details,
  fbm_flag,
  plink_flag,
  use_names = TRUE
)

Value

a matrix of estimated coeffcients, 'beta_vals', that is on the scale of the original data.

Arguments

std_scale_beta

The estimated coefficients on the standardized scale

p

The number of columns in the original design matrix

std_X_details

A list with 3 elements describing the standardized design matrix BEFORE rotation; this should have elements 'scale', 'center', and 'ns'

fbm_flag

Logical: is the corresponding design matrix filebacked?

plink_flag

Logical: did these data come from PLINK files? Note: This flag matters because of how non-genomic features are handled for PLINK files -- in data from PLINK files, unpenalized columns are not counted in the p argument. For delimited files, p does include unpenalized columns. This difference has implications for how the untransform() function determines the appropriate dimensions for the estimated coefficient matrix it returns.

use_names

Logical: should names be added? Defaults to TRUE. Set to FALSE inside of cvf() helper, as 'ns' will vary within CV folds.