Compute PCA from transformed expression data

Compute PCA from transformed expression data

Usage

compute_pca(expr_matrix, n_top = 500L, metadata = NULL)

Arguments

expr_matrix

Numeric matrix (genes x samples) of transformed expression values (e.g., VST or logCPM)

n_top

Number of most variable genes to use (default 500)

metadata

Optional data frame of sample annotations to merge with PCA coordinates

Value

List with components: coords (data frame with PC1, PC2, ...), var_explained (numeric vector of variance proportions), n_genes_used

See also

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