covfam: CovBat Family Harmonization

In ComBatFamQC: Comprehensive Batch Effect Diagnostics and Harmonization

CovBat Family Harmonization

Description

Implementation of the CovBat Family of harmonization methods allowing for removal of multivariate batch effects, flexible covariate modeling and alternative estimators for site effect adjustment. Support for modeling of both location and scale via GAMLSS. Additional support for modeling of covariate effects in score location and scale.

Usage

covfam(
  data,
  bat,
  covar = NULL,
  model = lm,
  formula = NULL,
  score.model = NULL,
  score.args = NULL,
  eb = TRUE,
  robust.LS = FALSE,
  ref.batch = NULL,
  percent.var = 0.95,
  n.pc = NULL,
  std.var = TRUE,
  ...
)

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
score.model	Model for scores, defaults to NULL for fitting basic location and scale model without covariates on the scores
score.args	List of arguments for score model
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. Uses median and biweight midvariance
ref.batch	Reference batch, must take value in levels(bat)
percent.var	Numeric. The number of harmonized principal component scores is selected to explain this proportion of the variance
n.pc	Optional numeric. If specified, this number of principal component scores is harmonized. Overrides percent.var
std.var	If TRUE, scales variances to be equal to 1 before PCA.
...	Additional arguments to model

Value

covfam returns a list containing the following components:

dat.covbat	Harmonized data as a matrix with same dimensions as data
batch.info	Batch information, including reference batch if specified
combat.out	List output of comfam from the ComBat step
pc.output	Output of prcomp from PCA step
n.pc	Numeric, number of PCs harmonized
scores.com	List output of comfam from the CovBat step

Examples

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

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