methyLImp2
This package is for version 3.20 of Bioconductor; for the stable, up-to-date release version, see methyLImp2.
Missing value estimation of DNA methylation data
Bioconductor version: 3.20
This package allows to estimate missing values in DNA methylation data. methyLImp method is based on linear regression since methylation levels show a high degree of inter-sample correlation. Implementation is parallelised over chromosomes since probes on different chromosomes are usually independent. Mini-batch approach to reduce the runtime in case of large number of samples is available.
Author: Pietro Di Lena [aut]
, Anna Plaksienko [aut, cre]
, Claudia Angelini [aut]
, Christine Nardini [aut]
Maintainer: Anna Plaksienko <anna at plaxienko.com>
citation("methyLImp2")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("methyLImp2")
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("methyLImp2")| methyLImp2 vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DNAMethylation, MethylationArray, Microarray, Regression, Software |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (1 year) |
| License | GPL-3 |
| Depends | R (>= 4.3.0), ChAMPdata |
| Imports | BiocParallel, parallel, stats, methods, corpcor, SummarizedExperiment, utils |
| System Requirements | |
| URL | https://github.com/annaplaksienko/methyLImp2 |
| Bug Reports | https://github.com/annaplaksienko/methyLImp2/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, spelling, testthat (>= 3.0.0) |
| 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 | methyLImp2_1.2.0.tar.gz |
| Windows Binary (x86_64) | methyLImp2_1.2.0.zip (64-bit only) |
| macOS Binary (x86_64) | methyLImp2_1.2.0.tgz |
| macOS Binary (arm64) | methyLImp2_1.2.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/methyLImp2 |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/methyLImp2 |
| Bioc Package Browser | https://code.bioconductor.org/browse/methyLImp2/ |
| Package Short Url | https://bioconductor.org/packages/methyLImp2/ |
| Package Downloads Report | Download Stats |