comfam: ComBat Family Harmonization

In ComBatFamQC: Comprehensive Batch Effect Diagnostics and Harmonization

ComBat Family Harmonization

Description

Implementation of the ComBat Family of harmonization methods allowing for flexible covariate modeling and alternative estimators for site effect adjustment. Support for modeling of both location and scale via GAMLSS and longitudinal harmonization via mixed effects models.

Usage

comfam(
  data,
  bat,
  covar = NULL,
  model = lm,
  formula = NULL,
  eb = TRUE,
  robust.LS = FALSE,
  ref.batch = NULL,
  ...
)

Arguments

data	n x p data frame or matrix of observations where p is the number of features and n is the number of subjects.
bat	Factor indicating batch (often equivalent to site or scanner)
covar	Data frame or matrix of covariates supplied to model
model	Model function. ComBat Family supports any models that take arguments formula and data, but are limited to models fitting with identity link (e.g. family = gaussian(link = "identity")). This includes lm, gam, gamlss, rq, lmer, and more
formula	Formula for model starting with ⁠y ~⁠ where y represents each feature
eb	If TRUE, uses ComBat model with empirical Bayes for mean and variance harmonization
robust.LS	If TRUE, uses robust location and scale estimators for error variance and site effect parameters. Currently uses median and biweight midvariance
ref.batch	Reference batch, must take value in levels(bat)
...	Additional arguments to model

Value

comfam returns a list containing the following components:

dat.combat	Harmonized data as a matrix with same dimensions as data
batch.info	Batch information, including reference batch if specified
fits	List of model fits from regression step, outputs of model for each feature
estimates	List of estimates from standardization and batch effect correction

See Also

predict.comfam for applying ComBat parameters for harmonization of new observations

Examples

comfam(iris[,1:2], iris$Species)
comfam(iris[,1:2], iris$Species, iris[3:4], lm, y ~ Petal.Length + Petal.Width)

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