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methyLImp2
This is thedevelopment version of methyLImp2; for the stable release version, seemethyLImp2.
Missing value estimation of DNA methylation data
Bioconductor version: Development (3.23)
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]
ORCID: 0000-0002-1838-8918, Anna Plaksienko [aut, cre] ORCID: 0000-0001-9607-057X, Claudia Angelini [aut] ORCID: 0000-0001-8350-8464, Christine Nardini [aut] ORCID: 0000-0001-7601-321X
Maintainer: Anna Plaksienko <anna at plaxienko.com>
citation("methyLImp2")):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("methyLImp2")For older versions of R, please refer to the appropriateBioconductor 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 | 1.7.1 |
| In Bioconductor since | BioC 3.19 (R-4.4) (1.5 years) |
| 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
FollowInstallation instructions to use this package in your R session.
| Source Package | methyLImp2_1.7.1.tar.gz |
| Windows Binary (x86_64) | methyLImp2_1.7.1.zip |
| macOS Binary (x86_64) | methyLImp2_1.7.1.tgz |
| macOS Binary (arm64) | methyLImp2_1.7.1.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 |