residual_gen: Post Harmonization Residual Generation

In ComBatFamQC: Comprehensive Batch Effect Diagnostics and Harmonization

Post Harmonization Residual Generation

Description

Extract residuals after harmonization.

Usage

residual_gen(
  type = "lm",
  features = NULL,
  covariates = NULL,
  interaction = NULL,
  random = NULL,
  smooth = NULL,
  smooth_int_type = NULL,
  df,
  rm = NULL,
  model = FALSE,
  model_path = NULL,
  cores = detectCores()
)

Arguments

type	A model function name that is to be used (eg: "lmer", "lm", "gam").
features	The names of the features from which to extract residuals.
covariates	Name of covariates supplied to model.
interaction	Expression of interaction terms supplied to model (eg: "age,diagnosis").
random	Variable name of a random effect in linear mixed effect model.
smooth	Variable name that requires a smooth function.
smooth_int_type	Indicates the type of interaction in gam models. By default, smooth_int_type is set to be "linear", representing linear interaction terms. "categorical-continuous", "factor-smooth" both represent categorical-continuous interactions ("factor-smooth" includes categorical variable as part of the smooth), "tensor" represents interactions with different scales, and "smooth-smooth" represents interaction between smoothed variables.
df	Harmonized dataset to extract residuals from.
rm	variables to remove effects from.
model	A boolean variable indicating whether an existing model is to be used.
model_path	path to the existing model.
cores	number of cores used for parallel computing.

Value

residual_gen returns a list containing the following components:

model	a list of regression models for all rois
residual	Residual dataframe

Examples

features <- colnames(adni)[43:53]
residual_gen(type = "lm", features = features,
covariates = c("AGE", "SEX", "DIAGNOSIS"), df = adni, rm = c("AGE", "SEX"), cores = 1)

ComBatFamQC documentation built on April 4, 2025, 12:24 a.m.