ComBatFamQC (version 1.0.5)

covfam: 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,
  ...
)

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

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

Examples

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