Package: randRotation 1.25.0

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]

randRotation_1.25.0.tar.gz
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randRotation_1.25.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
randRotation/json (API)

# 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-1.25.0(bioc 3.24)randRotation-1.23.0(bioc 3.23)

software sequencing batcheffect biomedicalinformatics rnaseq preprocessing microarray differentialexpression geneexpression genetics micrornaarray normalization statisticalmethod

3.60 score 3 scripts 12 exports 2 dependencies

Last updated from:6f4dc85f9f. Checks:1 WARNING, 6 ERROR, 2 OK, 1 NOTE. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	164
linux-devel-x86_64	ERROR	210
source / vignettes	OK	283
linux-release-x86_64	ERROR	223
macos-release-arm64	ERROR	119
macos-oldrel-arm64	ERROR	96
windows-devel	ERROR	123
windows-release	ERROR	114
windows-oldrel	NOTE	132
wasm-release	OK	170

Exports:contrastModel initBatchRandrot initRandrot pFdr qqunif randorth randpermut randrot rotateStat show weights X_decomp

Dependencies:rbibutils Rdpack

Random Rotation Package Introduction

Rendered fromrandRotationIntro.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
randRotation: Random Rotation Methods for High Dimensional Data with Batch Structure	randRotation-package randRotation
Create transformed model matrix for contrast rotation	contrastModel
Dimensions of an Object	dim,initBatchRandrot-method dim,initRandrot-method
Dimnames of an Object	dimnames,initBatchRandrot-method dimnames,initRandrot-method
Initialised random rotation batch object	initBatchRandrot-class
Initialisation of a random rotation Object	initBatchRandrot initBatchRandrot,list-method initRandrot initRandrot,list-method
Initialised random rotation class	initRandrot-class initRandrotW-class
Calculate resampling based p-values and FDRs	pFdr
Quantile-Quantile plot of data sample against uniform theoretical quantiles	qqunif
Random orthogonal matrix	randorth
Generate random permutation matrix for n samples	randpermut
Random rotation of initialised object	randrot randrot,initBatchRandrot-method randrot,initRandrot-method randrot,initRandrotW-method
Defunct functions in package 'randRotation'	df_estimate
Generate data rotations and calculate statistics on it	rotateStat
Rotated object containing rotated and non-rotated statistics	rotateStat-class
Show an Object	show,initBatchRandrot-method show,initRandrot-method show,rotateStat-method
Extract model weights	weights,initBatchRandrot-method weights,initRandrot-method
Decomposition of the design matrix for random rotation generation	X_decomp