ComBatFamQC (version 1.0.5)

residual_gen: 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()
)

Value

residual_gen returns a list containing the following components:

model

a list of regression models for all rois

residual

Residual dataframe

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.

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)