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Calculates PCA for single cell

rs_sc_pca.Rd

Helper function that will calculate the PCA for the specified highly variable genes. Has the option to use randomised SVD for faster solving of the PCA.

Usage

rs_sc_pca(
  f_path_gene,
  no_pcs,
  random_svd,
  cell_indices,
  gene_indices,
  seed,
  return_scaled,
  verbose
)

Arguments

f_path_gene

String. Path to the counts_genes.bin file.

no_pcs

Integer. Number of PCs to calculate.

random_svd

Boolean. Shall randomised SVD be used.

cell_indices

Integer. The cell indices to use. (0-indexed!)

gene_indices

Integer. The gene indices to use. (0-indexed!)

seed

Integer. Random seed for the randomised SVD.

return_scaled

Boolean. Shall the scaled data be returned.

verbose

Boolean. Controls verbosity of the function.

Value

A list with with the following items

  • scores - The samples projected on the PCA space.

  • loadings - The loadings of the features for the PCA.

  • singular_values - The singular values for the PCA.

  • scaled - The scaled matrix if you set return_scaled to TRUE.