Run variance stabilizing transformation

Wrapper around DESeq2::vst() for use in visualization. VST is appropriate for PCA, heatmaps, and clustering – not for DE testing (which uses raw counts).

Usage

run_vst(se_data, blind = TRUE)

Arguments

se_data

SummarizedExperiment with "counts" assay

blind

Logical, whether VST should be blind to the design (default TRUE for exploratory analysis)

Value

SummarizedExperiment with "vst" assay added, or NULL if DESeq2 is not available

See also

Other differential-expression: compute_pca(), plot_heatmap_de(), plot_ma(), plot_pca(), plot_volcano(), run_deseq2(), summarize_de_methods()