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rrda (version 0.2.3)

Ridge Redundancy Analysis for High-Dimensional Omics Data

Description

Efficient framework for ridge redundancy analysis (rrda), tailored for high-dimensional omics datasets where the number of predictors exceeds the number of samples. The method leverages Singular Value Decomposition (SVD) to avoid direct inversion of the covariance matrix, enhancing scalability and performance. It also introduces a memory-efficient storage strategy for coefficient matrices, enabling practical use in large-scale applications. The package supports cross-validation for selecting regularization parameters and reduced-rank dimensions, making it a robust and flexible tool for multivariate analysis in omics research. Please refer to our article (Yoshioka et al., 2025) for more details.

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Version

Install

install.packages('rrda')

Monthly Downloads

160

Version

0.2.3

License

GPL (>= 3)

Maintainer

Julie Aubert

Last Published

October 15th, 2025

Functions in rrda (0.2.3)

rrda.plot

Plot the results of cross-validation for Bhat obtained from the rrda.cv function.
rrda.predict

Calculate the predicted matrix Yhat using the coefficient Bhat obtained from the rrda.fit function.
get_Bhat_comp

Compute the components of the coefficient Bhat using SVD.
rrda.summary

Summarize the results of cross-validation for the coefficient Bhat obtained from the rrda.cv function.
unbiased_scale

Scale a matrix using unbiased estimators for the mean and standard deviation.
rrda.top

Top feature interactions visualization with rank and lambda penalty
get_rlist

Generate rank-specific matrices by combining the left and right components.
rdasim1

Generate simulated data for Ridge Redundancy Analysis (RDA).
rdasim2

Generate simulated data for Ridge Redundancy Analysis (RDA).
rrda.cv

Cross-validation for Ridge Redundancy Analysis
Bhat_mat_rlist

Generate a list of rank-specific Bhat matrices (the coefficient of Ridge Redundancy Analysis for each parameter lambda and nrank).
get_lambda

Estimate an appropriate value for the ridge penalty (lambda).
rrda.coef

Calculate the Bhat matrix from the return of the rrda.fit function.
unscale_matrices

Unscale a matrix based on provided mean and standard deviation values.
rrda.heatmap

Heatmap of the results of cross-validation for Bhat obtained from the rrda.cv function.
unscale_nested_matrices_map

Apply unscaling to a nested list of matrices using specified mean and standard deviation values.
rrda.fit

Calculate the coefficient Bhat by Ridge Redundancy Analysis.
Yhat_mat_rlist

Generate a list of rank-specific Yhat matrices.
MSE_lambda_rank

Compute MSE for different ranks of the coefficient Bhat and lambda.
sqrt_inv_d2_lambda

Compute the square root of the inverse of (d^2 + lambda).