Run DESeq2 differential expression analysis — run_deseq2 • coMMpass

Runs DESeq2 with optional apeglm log-fold-change shrinkage and optional paired longitudinal design for within-patient comparisons.

Usage

run_deseq2(
  se_data,
  clinical_data,
  design_formula = ~condition,
  shrink_lfc = TRUE,
  paired = FALSE
)

Arguments

se_data: A SummarizedExperiment object
clinical_data: Clinical data frame
design_formula: Design formula for the model
shrink_lfc: If TRUE, apply apeglm LFC shrinkage (default TRUE)
paired: If TRUE, use paired longitudinal design with patient as blocking factor. Requires 'patient_id' and 'visit' columns in clinical_data. Only patients with >=2 timepoints are included.

Value

List with DE results including raw and shrunken (if requested)

See also

Other differential-expression: compute_pca(), plot_heatmap_de(), plot_ma(), plot_pca(), plot_volcano(), run_vst(), summarize_de_methods()