Package: randRotation 1.19.0

Peter Hettegger

randRotation: Random Rotation Methods for High Dimensional Data with Batch Structure

A collection of methods for performing random rotations on high-dimensional, normally distributed data (e.g. microarray or RNA-seq data) with batch structure. The random rotation approach allows exact testing of dependent test statistics with linear models following arbitrary batch effect correction methods.

Authors:Peter Hettegger [aut, cre]

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randRotation.pdf |randRotation.html✨
randRotation/json (API)
NEWS

# Install 'randRotation' in R:
install.packages('randRotation', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/phettegger/randrotation/issues

On BioConductor:randRotation-1.19.0(bioc 3.21)randRotation-1.18.0(bioc 3.20)

softwaresequencingbatcheffectbiomedicalinformaticsrnaseqpreprocessingmicroarraydifferentialexpressiongeneexpressiongeneticsmicrornaarraynormalizationstatisticalmethod

3.60 score 3 scripts 178 downloads 12 exports 2 dependencies

Last updated 4 months agofrom:f41d79e022. Checks:1 OK, 4 ERROR, 3 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 25 2025
R-4.5-winNOTEFeb 25 2025
R-4.5-macERRORFeb 25 2025
R-4.5-linuxERRORFeb 25 2025
R-4.4-winNOTEFeb 25 2025
R-4.4-macERRORFeb 25 2025
R-4.3-winNOTEFeb 25 2025
R-4.3-macERRORFeb 25 2025

Exports:contrastModelinitBatchRandrotinitRandrotpFdrqqunifrandorthrandpermutrandrotrotateStatshowweightsX_decomp

Dependencies:rbibutilsRdpack

Random Rotation Package Introduction

Peter Hettegger

Rendered fromrandRotationIntro.Rmdusingknitr::rmarkdownon Feb 25 2025.

Last update: 2021-02-09
Started: 2020-01-03

Readme and manuals

Help Manual

Help pageTopics
randRotation: Random Rotation Methods for High Dimensional Data with Batch StructurerandRotation-package randRotation
Create transformed model matrix for contrast rotationcontrastModel
Dimensions of an Objectdim,initBatchRandrot-method dim,initRandrot-method
Dimnames of an Objectdimnames,initBatchRandrot-method dimnames,initRandrot-method
Initialised random rotation batch objectinitBatchRandrot-class
Initialisation of a random rotation ObjectinitBatchRandrot initBatchRandrot,list-method initRandrot initRandrot,list-method
Initialised random rotation classinitRandrot-class initRandrotW-class
Calculate resampling based p-values and FDRspFdr
Quantile-Quantile plot of data sample against uniform theoretical quantilesqqunif
Random orthogonal matrixrandorth
Generate random permutation matrix for n samplesrandpermut
Random rotation of initialised objectrandrot randrot,initBatchRandrot-method randrot,initRandrot-method randrot,initRandrotW-method
Defunct functions in package 'randRotation'df_estimate
Generate data rotations and calculate statistics on itrotateStat
Rotated object containing rotated and non-rotated statisticsrotateStat-class
Show an Objectshow,initBatchRandrot-method show,initRandrot-method show,rotateStat-method
Extract model weightsweights,initBatchRandrot-method weights,initRandrot-method
Decomposition of the design matrix for random rotation generationX_decomp