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Compute PCA on Single-Slide Data

Source: R/13_compute_PCA.R
computePCA.Rd

This method performs PCA on the normalized data stored within the CoProSingle object. It assumes that the data has already been integrated across slides.

This method performs PCA on the normalized data stored within the CoProMulti object. It assumes that the data has already been integrated across slides.

Usage

# S4 method for class 'CoProSingle'
computePCA(object, nPCA = 40, center = TRUE, scale. = TRUE, scalePCs = TRUE)

# S4 method for class 'CoProMulti'
computePCA(
  object,
  nPCA = 40,
  center = TRUE,
  scale. = TRUE,
  scalePCs = TRUE,
  dataUse = "raw",
  center_per_slide = FALSE
)

Arguments

object

A CoProMulti object with the normalizedData 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).

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