Fit a limma-voom differential-expression model

Usage

de_voom(
  x,
  experiment,
  formula,
  assay = "counts",
  filter = TRUE,
  normalize_method = "TMM",
  contrasts = NULL,
  trend = FALSE,
  voom_plot = FALSE,
  ...
)

Arguments

x: A MultiAssayExperiment object.
experiment: Optional experiment name.
formula: Fixed-effect model formula.
assay: Assay name or one-based assay index.
filter: Remove low-expression features with edgeR::filterByExpr().
normalize_method: Library normalization method.
contrasts: Optional contrast matrix passed to limma::contrasts.fit().
trend: Passed to limma::eBayes().
voom_plot: Draw the voom mean-variance diagnostic plot.
...: Additional arguments passed to limma::eBayes().

Value

A native MArrayLM object.