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regionalpcs
This is thedevelopment version of regionalpcs; for the stable release version, seeregionalpcs.
Summarizing Regional Methylation with Regional Principal Components Analysis
Bioconductor version: Development (3.23)
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]
ORCID: 0000-0002-7084-9646
Maintainer: Tiffany Eulalio <tyeulalio at gmail.com>
citation("regionalpcs")):Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")# The following initializes usage of Bioc develBiocManager::install(version='devel')BiocManager::install("regionalpcs")For older versions of R, please refer to the appropriateBioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | DNAMethylation,DifferentialMethylation,MethylationArray,Software,StatisticalMethod |
| Version | 1.9.0 |
| In Bioconductor since | BioC 3.18 (R-4.3) (2 years) |
| 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 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
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| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | regionalpcs_1.9.0.zip (64-bit only) |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/regionalpcs |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/regionalpcs |
| Package Short Url | https://bioconductor.org/packages/regionalpcs/ |
| Package Downloads Report | Download Stats |