methyLImp2
This is the released version of methyLImp2; for the devel version, see methyLImp2.
Missing value estimation of DNA methylation data
Bioconductor version: Release (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]
, Anna Plaksienko [aut, cre]
, Claudia Angelini [aut]
, Christine Nardini [aut]
Maintainer: Anna Plaksienko <anna at plaxienko.com>
citation("methyLImp2")):
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")
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 | 1.8.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (2.5 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
Follow Installation instructions to use this package in your R session.
| Source Package | methyLImp2_1.8.0.tar.gz |
| Windows Binary (x86_64) | methyLImp2_1.8.0.zip |
| macOS Binary (big-sur-x86_64) | methyLImp2_1.8.0.tgz |
| macOS Binary (sonoma-arm64) | methyLImp2_1.8.0.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 |