RepeatedHighDim: RepeatedHighDim Package

In RepeatedHighDim: Methods for High-Dimensional Repeated Measures Data

RepeatedHighDim Package

Description

A comprehensive toolkit for repeated high-dimensional analysis.

Details

The RepeatedHighDim-package is a collection of functions for the analysis of high-dimensional repeated measures data, e.g. from Omics experiments. It provides function for outlier detection, differential expression analysis, self-contained gene-set testing, and generation of correlated binary data.

For more information and examples, please refer to the package documentation and the tutorial available at https://software.klausjung-lab.de/.

Functions

This package includes the following functions:

B:

• bag: Calculates the bag.

D:

• depmed: Calculates the depth median.

F:

• fc_ci: Calculates adjusted confidence intervals.

• fc_plot: Creates a volcano plot of adjusted confidence intervals.

G:

• GA_diagplot: Generates a diagnostic plot for comparing two correlation matrices.

• gem: Plots a gemstone to an interactive graphics device.

• GlobTestMissing: Detects global group effects.

• gridfun: Specifies a grid for calculating halfspace location depths.

H:

• hldepth: Calculates the halfspace location depth.

I:

• iter_matrix: Implements a genetic algorithm for generating correlated binary data.

L:

• loop: Calculates the fence and the loop.

N:

• netRNA: network meta-analysis using gene expression data.

R:

• RHighDim: Detects global group effects.

• rho_bounds: Calculates lower and upper bounds for pairwise correlations.

• rmvbinary_EP: Simulates correlated binary variables using the algorithm by Emrich and Piedmonte (1991).

• rmvbinary_QA: Simulates correlated binary variables using the algorithm by Qaqish (2003).

S:

• scTC_bpplot: Post-trim breakpoint heatmap for scTrimClust results.

• scTC_trim_effect: Compare scTrimClust trimming against default Seurat analysis.

• scTrimClust: Clustering with alpha hull-based outlier detection.

• sequence_probs: Calculates probabilities for binary sequences.

• start_matrix: Sets up the start matrix.

• summary_RHD: Provides a summary of the RHighDim function.

Author(s)

Maintainer: Klaus Jung ([e-mail])

Other contributors:

• Jochen Kruppa ([e-mail])

• Sergej Ruff ([e-mail] ,second maintainer)

If you have any questions, suggestions, or issues, please feel free to contact the maintainer, Klaus Jung ([e-mail]).

See Also

For more information, please refer to the package's documentation and the tutorial: https://software.klausjung-lab.de/.

RepeatedHighDim documentation built on April 15, 2025, 1:28 a.m.