permut_pca_V.princals: Permutation PCA sample permV princals

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

Permutation PCA sample permV princals

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 'princals'
permut_pca_V(pca, x, output, original_loadings, ndim, pb = NULL, ...)

Arguments

pca	Object of class princals.
x	Data passed to the princals.
output	Character. Determines the output to compute. Possible values are Variance accounted for ("VAF"), the standardized loadings ("s.loadings") or communalities.
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 26, 2022, 5:36 p.m.