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 (3.24)
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("regionalpcs")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DNAMethylation, DifferentialMethylation, MethylationArray, Software, StatisticalMethod |
| Version | 1.11.0 |
| In Bioconductor since | BioC 3.18 (R-4.3) (3 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 | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | regionalpcs_1.11.0.tar.gz |
| Windows Binary (x86_64) | regionalpcs_1.11.0.zip |
| macOS Binary (big-sur-x86_64) | regionalpcs_1.11.0.tgz |
| macOS Binary (sonoma-arm64) | regionalpcs_1.11.0.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 |