Run PCA — run_pca • scooter

The default method runs irlba::prcomp_irlba() on a matrix; the Seurat method runs Seurat::RunPCA() on the object and stores a "pca<suffix>" reduction.

Usage

run_pca(x, ...)

# Default S3 method
run_pca(x, num_pcs = 50, suffix = "", ...)

# S3 method for class 'Seurat'
run_pca(
  x,
  num_pcs = 50,
  suffix = "",
  assay = "RNA",
  features = NULL,
  var_features = FALSE,
  ...
)

Arguments

x: A matrix (default) or a Seurat object.
...: Passed to the underlying function.
num_pcs: Number of principal components.
suffix: Tag inserted into the reduction/column names.
assay: Assay to use (Seurat method). Always set explicitly.
features: Explicit features to use (Seurat method).
var_features: Use the assay's variable features (Seurat method).

Value

A named list (default) or a Seurat object with the reduction added (Seurat method). The Seurat method also writes the diagnostic plots to the working directory: a sample-colored scatter and an elbow plot, plus a heatmap past 15 components.