Compute PCA on Integrated Multi-Slide Data

Performs PCA on the integrated data stored within the CoProMulti object. Assumes integration has created a common space across slides.

Usage

computePCA(
  object,
  nPCA = 40,
  center = TRUE,
  scale. = TRUE,
  scalePCs = TRUE,
  dataUse = "raw",
  center_per_slide = FALSE
)

object: A CoProMulti object with the integratedData slot populated.
nPCA: Number of principal components to compute for each cell type.
center: Whether to center the matrix before PCA
scale.: Whether to scale the matrix before PCA
scalePCs: Whether to scale (whiten) PCs by their standard deviation before downstream CCA optimization. Default TRUE (recommended). When PCs are whitened, the unit-norm constraint ||w|| = 1 is equivalent to the standard CCA constraint ||w'X'Xw|| = 1. Setting this to FALSE distorts the constraint space and may produce unreliable results.
dataUse: What data to use, choices between "raw" and "integrated". Default is "raw". For single slide, this argument is ignored.
center_per_slide: After the global PCA, do we do center per slide again? By default this is set to FALSE

A CoProMulti object with the pcaResults slot populated. pcaResults structure: list(slideID = list(cellType = pc_matrix)).