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Wrapper for PCA specifically designed for single cells

params_sc_pca.Rd

Wrapper for PCA specifically designed for single cells

Usage

params_sc_pca(
  mean_center = TRUE,
  normalise_variance = TRUE,
  randomised = TRUE,
  clr = FALSE,
  size_factor = 10000
)

Arguments

mean_center

Boolean. Shall the data be mean centred Defaults to TRUE.

normalise_variance

Boolean. Shall the data have normalised variance Defaults to TRUE.

randomised

Boolean. Shall fast, approximate randomised SVD be used. Defaults to TRUE.

clr

Boolean. Shall the CLR-type PFlogPF be applied, see Booeshaghi, et al. Defaults to FALSE.

size_factor

Numeric. The used size factor during I/O. It needs to be the same as during I/O to have correct results when using the PFlogPF transformation. Defaults to 10000.0.

Value

A named list with the following elements:

  • mean_center - Boolean. Shall the data be mean centred Defaults to TRUE.

  • normalise_variance - Boolean. Shall the data have normalised variance Defaults to TRUE.

  • randomised - Boolean. Shall fast, approximate randomised SVD be used. Defaults to TRUE.

  • clr - Boolean. Shall the CLR-type PFlogPF be applied, see Booeshaghi, et al. Defaults to FALSE.

  • size_factor - Numeric. The used size factor during I/O. It needs to be the same as during I/O to have correct results when using the PFlogPF transformation. Defaults to 10000.0.