regionalpcs
Summarizing Regional Methylation with Regional Principal Components Analysis
Bioconductor version: 3.24 · Package version: 1.11.0
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("regionalpcs")Details
| Maintainer | Tiffany Eulalio <tyeulalio@gmail.com> |
| Author | Tiffany Eulalio [aut, cre] (ORCID: <https://orcid.org/0000-0002-7084-9646>) |
| License | MIT + file LICENSE |
| URL | https://github.com/tyeulalio/regionalpcs |
| Bug Reports | https://github.com/tyeulalio/regionalpcs/issues |
| Downloads rank | 279 |
| Source branch | devel |
| biocViews | DNAMethylation, DifferentialMethylation, MethylationArray, Software, StatisticalMethod |
Documentation
Download
Follow the 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 (arm64) | regionalpcs_1.11.0.tgz |
| macOS binary (x86_64) | regionalpcs_1.11.0.tgz |
Dependencies
Depends: R (>= 4.3.0)
Imports: dplyr, PCAtools, tibble, GenomicRanges
Suggests: knitr, rmarkdown, RMTstat, testthat (>= 3.0.0), BiocStyle, tidyr, minfiData, TxDb.Hsapiens.UCSC.hg19.knownGene, IRanges