Package index

Core decomposition

Run the RaJIVE decomposition and simulate data.

Rajive()

Robust Angle based Joint and Individual Variation Explained

ajive.data.sim()

Simulation of data blocks

sim_dist()

Simulation of single data block from distribution

Rank accessors

Extract rank estimates from a rajive object.

get_joint_rank()

Joint Rank

get_individual_rank()

Individual Rank

get_all_ranks()

Summary table of all ranks

Component accessors

Extract scores, loadings, and reconstructed matrices.

get_joint_scores()

Joint Scores

get_block_scores()

Block Scores

get_block_loadings()

Block Loadings

get_block_matrix()

Extract a reconstructed block matrix

S3 methods for rajive objects

print and summary methods.

print(<rajive>)

Print method for rajive objects

summary(<rajive>)

Summary method for rajive objects

Variance explained

Quantify and visualise explained variance.

showVarExplained_robust()

Proportions of variance explained

plot_variance_explained()

Bar chart of variance explained

Visualisation

Heatmaps and score plots.

decomposition_heatmaps_robustH()

Decomposition Heatmaps

data_heatmap()

Decomposition Heatmaps

plot_scores()

Scatter plot of block scores

Internal decomposition helpers

Low-level functions used internally by Rajive() to compute joint and individual decompositions.

get_final_decomposition_robustH()

Computes the final JIVE decomposition.

get_individual_decomposition_robustH()

Computes the individual matrix for a data block.

get_joint_decomposition_robustH()

Computes the individual matrix for a data block

get_joint_scores_robustH()

Computes the joint scores.

Robust SVD utilities

Functions for computing, truncating, and reconstructing the robust SVD.

RobRSVD.all()

Computes the robust SVD of a matrix

RobRSVD1()

Single robust rank-1 component (Rcpp wrapper)

get_svd_robustH()

Computes the robust SVD of a matrix Using robRsvd

get_sv_threshold()

The singular value threshold.

truncate_svd()

Truncates a robust SVD.

svd_reconstruction()

Reconstruces the original matrix from its robust SVD.

Rank estimation internals

Wedin bound and random direction bound helpers used in joint rank estimation.

get_random_direction_bound_robustH()

Estimate the wedin bound for a data matrix.

get_wedin_bound_samples()

Gets the wedin bounds

wedin_bound_resampling()

Resampling procedure for the wedin bound

Jackstraw significance testing

Permutation-based test to identify variables with significantly non-zero joint loadings.

jackstraw_rajive()

Jackstraw significance testing for RaJIVE joint loadings

print(<jackstraw_rajive>)

Print method for jackstraw_rajive objects

summary(<jackstraw_rajive>)

Summary method for jackstraw_rajive objects

get_significant_vars()

Extract significant variables from jackstraw results

plot_jackstraw()

Plot jackstraw results

Package

Package-level documentation.

rajiveutils rajiveutils-package

rajiveutils: Robust Angle Based Joint and Individual Variation Explained