crossarrayEWAS
This is the development version of crossarrayEWAS; to use it, please install the devel version of Bioconductor.
Design-Aware Region and Block Detection for Cross-Array Longitudinal EWAS
Bioconductor version: Development (3.24)
Estimation and region-calling routines for epigenome-wide association studies that combine Illumina HumanMethylation450 and MethylationEPIC samples and follow subjects over more than one visit. Probe-level effects are fitted within subject, so subject identity, array type and chip are absorbed rather than modelled; adjacent probes are grouped by within-subject co-methylation; regions are obtained by total-variation denoising with a distance-decaying penalty, which places boundaries where the effect track jumps instead of thresholding a smooth curve; and long-range blocks are called from a three-state hidden semi-Markov model whose transition probabilities decay with genomic distance. Selection stability and permutation nulls resample subjects, not samples, so a subject's visit series is never split.
Author: Katarzyna Kamieniecka [aut, cre] 
, Samantha McLean [aut] , Krzysztof Poterlowicz [aut]
Maintainer: Katarzyna Kamieniecka <kkamieni at bradford.ac.uk>
citation("crossarrayEWAS")):Katarzyna Kamieniecka, Samantha McLean, Krzysztof Poterlowicz. crossarrayEWAS: Design-Aware Region and Block Detection for Cross-Array Longitudinal EWAS. doi:10.18129/B9.bioc.crossarrayEWAS, R package version 0.99.1, https://bioconductor.org/packages/crossarrayEWAS.
Generated from the package metadata; it may differ from the package's own citation.
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("crossarrayEWAS")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("crossarrayEWAS")| Design-aware region and block detection for cross-array longitudinal EWAS | HTML |
| Reference Manual | |
| NEWS | Text |
Details
| biocViews | DNAMethylation, DifferentialMethylation, Epigenetics, MethylationArray, Regression, Software |
| Version | 0.99.1 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.5.0) |
| Imports | GenomicRanges, IRanges, Matrix, S4Vectors, SummarizedExperiment, jsonlite, limma, methods, stats |
| System Requirements | |
| URL | https://github.com/bioinfbrad/crossarrayEWAS |
| Bug Reports | https://github.com/bioinfbrad/crossarrayEWAS/issues |
See More
| Suggests | testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle, minfi, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/crossarrayEWAS |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/crossarrayEWAS |
| Package Short Url | https://bioconductor.org/packages/crossarrayEWAS/ |
| Package Downloads Report | Download Stats |