Test Differential Expression — prot.test

This function tests for differential expression between conditions

Usage

prot.test_diff(
  se,
  type = c("control", "all", "manual"),
  control = NULL,
  test = NULL,
  design_formula = stats::formula(~0 + condition)
)

se: A SummarizedExperiment object
type: Character vector indicating which type of contrast to use. Options are: "control", "all" or "manual".
control: Character vector indicating the control condition. Required when type is "control".
test: Character vector indicating the contrasts to be tested. Required when type is "manual". Needs to be in the form "Subject_vs_Control".
design_formula: Formula object indicating the design of the experiment.

A SummarizedExperiment object with the results of the differential expression test that can be accessed with SummarizedExperiment::rowData(se)