HDTD-package {HDTD} | R Documentation

## Estimation and Hypothesis Testing in High-Dimensional Transposable Data

### Description

The package HDTD offers functions to estimate and test the matrix parameters of transposable data in high-dimensional settings.

### Details

The term transposable data refers to datasets that are structured in a matrix form such that both the rows and columns correspond to variables of interest. For example, consider microarray studies in genetics where multiple RNA samples across different tissues are available per subject. In this case, a data matrix can be created with row variables the genes, column variables the tissues and measurements the corresponding expression levels.

The function `meanmat.hat` estimates the mean matrix of the transposable data.

The mean relationship of the row and column variables can be tested using the function `meanmat.ts`. The implemented test is nonparametric and not seriously restricted by the dependence structure among and/or between the row and column variables. See Touloumis et al. (2015) for more details.

The function `covmat.hat` provides Stein-type shrinkage estimators for the row covariance matrix and/or for the column covariance matrix under a matrix-variate normal model. See Touloumis et al. (2016) for more details.

The sphericity and identity hypothesis for the row or column covariance matrix can be tested using the function `covmat.ts`. Both tests are nonparametric, i.e., they do not rely on a normality assumption. See Touloumis et al. (2017) for more details.

There are three utility functions that allow the user to change to interchange the role of row and column variables (`transposedata`), to center the transposable data (`centerdata`) or to rearrange the order of the row and/or column variables (`orderdata`).

### Author(s)

Anestis Touloumis, John Marioni, Simon Tavare.

Maintainer: Anestis.Touloumis <A.Touloumis@brighton.ac.uk>

### References

Touloumis, A., Tavare, S. and Marioni, J. C. (2015) Testing the Mean Matrix in High-Dimensional Transposable Data. Biometrics 71, 157–166

Touloumis, A., Marioni, J. C. and Tavare, S. (2016) HDTD: Analyzing multi-tissue gene expression data. Bioinformatics 32, 2193–2195.

Touloumis, A., Marioni, J. C. and Tavare, S. (2019+) Hypothesis Testing for the Covariance Matrix in High-Dimensional Transposable Data with Kronecker Product Dependence Structure. Statistica Sinica.

### Examples

    data(VEGFmouse)
    ## The sample mean matrix.
    sample_mean <- meanmat.hat(datamat = VEGFmouse, N = 40)
    sample_mean
    ## Testing conservation of the overall gene expression across tissues.
    tissues_mean_test <- meanmat.ts(datamat = VEGFmouse, N = 40, group.sizes = 9)
    tissues_mean_test
    # Estimating the gene and column covariance matrices.
    est_cov_mat <- covmat.hat(datamat = VEGFmouse, N = 40)
    est_cov_mat
    ## Hypothesis tests for the covariance matrix of the genes (rows).
    genes_cov_test <- covmat.ts(datamat = VEGFmouse, N = 40)
    genes_cov_test
    ## Hypothesis tests for the covariance matrix of the tissues (columns).
    tissues_cov_test <- covmat.ts(datamat = VEGFmouse, N = 40, voi = 'columns')
    tissues_cov_test

[Package HDTD version 1.24.0 Index]