Run CAMERA competitive gene-set testing — enrich

The selected assay must contain an approximately homoscedastic log-scale expression matrix. For voom analyses, supply the corresponding observation weights through weights; omitting them changes the intended mean-variance model.

Usage

enrich_camera(
  x,
  experiment,
  gene_sets,
  formula,
  contrast,
  assay,
  weights = NULL,
  ...
)

Arguments

x: A MultiAssayExperiment object.
experiment: Optional experiment name.
gene_sets: Named list of gene sets.
formula: Model formula used to construct the design matrix.
contrast: Contrast accepted by limma::camera().
assay: Assay name or one-based assay index.
weights: Optional observation-level precision-weight matrix, or the name of an assay containing one. It must have the same dimensions and dimnames as assay. When omitted, no voom precision weights are used.
...: Additional arguments passed to limma::camera().

Value

The native CAMERA result data frame.