permut_pca_V.prcomp: Permutation PCA sample permV prcomp

In ucsf-ferguson-lab/syndRomics: Component loading interpretation and visualization with syndromic plots

Permutation PCA sample permV prcomp

Description

Generates a permuted sample from a PCA that can be used for nonparametric permutation test (see permut_pc_test).

Usage

## S3 method for class 'prcomp'
permut_pca_V(
  pca,
  x,
  output,
  center,
  .scale,
  original_loadings,
  ndim,
  pb = NULL,
  ...
)

Arguments

pca	Object of class prcomp
x	Data passed to the prcomp.
output	Character. Determines the output to compute. Possible values are Variance accounted for ("VAF"), the standardized loadings ("s.loadings") or communalities.
center	Logical. Whether pca is conducted on the centered data.
.scale	Logical. Whether pca is conducted on the scaled data.
original_loadings	The data.frame containing the standardized loadings of the original sample.
ndim	Numeric. Number of PCs to save (1 to ndim).
pb	Object of class "Progress_bar" "R6" generated by progress::progress_bar$new(). Not required.
...	Not in use

Details

This is a helper function internally called by permut_pca_test() to produce a permutation sample of the given output of the prcomp()

Author(s)

Abel Torres Espin

References

1. Buja A, Eyuboglu N. Remarks on Parallel Analysis. Multivar Behav Res. 1992 Oct 1;27(4):509–40

2. Linting M, van Os BJ, Meulman JJ. Statistical Significance of the Contribution of Variables to the PCA solution: An Alternative Permutation Strategy. Psychometrika. 2011 Jul 1;76(3):440–60

ucsf-ferguson-lab/syndRomics documentation built on June 12, 2025, 3:04 p.m.