regionalpcs

DOI: 10.18129/B9.bioc.regionalpcs  

Summarizing Regional Methylation with Regional Principal Components Analysis

Bioconductor version: Release (3.18)

Functions to summarize DNA methylation data using regional principal components. Regional principal components are computed using principal components analysis within genomic regions to summarize the variability in methylation levels across CpGs. The number of principal components is chosen using either the Marcenko-Pasteur or Gavish-Donoho method to identify relevant signal in the data.

Author: Tiffany Eulalio [aut, cre]

Maintainer: Tiffany Eulalio <tyeulalio at gmail.com>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("regionalpcs")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("regionalpcs")

 

HTML	R Script	regionalpcs
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	DNAMethylation, DifferentialMethylation, MethylationArray, Software, StatisticalMethod
Version	1.0.0
In Bioconductor since	BioC 3.18 (R-4.3) (< 6 months)
License	MIT + file LICENSE
Depends	R (>= 4.3.0)
Imports	dplyr, PCAtools, tibble, GenomicRanges
LinkingTo
Suggests	knitr, rmarkdown, RMTstat, testthat (>= 3.0.0), BiocStyle, tidyr, minfiData, TxDb.Hsapiens.UCSC.hg19.knownGene, IRanges
SystemRequirements
Enhances
URL	https://github.com/tyeulalio/regionalpcs
BugReports	https://github.com/tyeulalio/regionalpcs/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	regionalpcs_1.0.0.tar.gz
Windows Binary	regionalpcs_1.0.0.zip
macOS Binary (x86_64)	regionalpcs_1.0.0.tgz
macOS Binary (arm64)	regionalpcs_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/regionalpcs
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/regionalpcs
Bioc Package Browser	https://code.bioconductor.org/browse/regionalpcs/
Package Short Url	https://bioconductor.org/packages/regionalpcs/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.18	Source Archive