Fit an edgeR quasi-likelihood model

Usage

de_edger(
  x,
  experiment,
  formula,
  assay = "counts",
  filter = TRUE,
  normalize_method = "TMM",
  robust = TRUE,
  coef = NULL,
  contrast = NULL,
  ...
)

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.
robust: Use robust empirical Bayes dispersion estimation.
coef: Coefficient index or name for edgeR::glmQLFTest().
contrast: Optional numeric contrast for edgeR::glmQLFTest().
...: Additional arguments passed to edgeR::glmQLFit().

Value

A native DGEGLM fit when neither coef nor contrast is given; otherwise a native DGELRT test object.