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regionalpcs

This is the development version of regionalpcs; for the stable release version, see regionalpcs.

Summarizing Regional Methylation with Regional Principal Components Analysis


Bioconductor version: Development (3.19)

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>

Citation (from within R, enter citation("regionalpcs")):

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
regionalpcs HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews DNAMethylation, DifferentialMethylation, MethylationArray, Software, StatisticalMethod
Version 1.1.0
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
System Requirements
URL https://github.com/tyeulalio/regionalpcs
Bug Reports https://github.com/tyeulalio/regionalpcs/issues
See More
Suggests knitr, rmarkdown, RMTstat, testthat (>= 3.0.0), BiocStyle, tidyr, minfiData, TxDb.Hsapiens.UCSC.hg19.knownGene, IRanges
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Package Archives

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

Source Package regionalpcs_1.1.0.tar.gz
Windows Binary regionalpcs_1.1.0.zip
macOS Binary (x86_64) regionalpcs_1.1.0.tgz
macOS Binary (arm64) regionalpcs_1.1.0.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