methyLImp2
Missing value estimation of DNA methylation data
Bioconductor version: 3.23 · Package version: 1.8.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("methyLImp2")Details
| Maintainer | Anna Plaksienko <anna@plaxienko.com> |
| Author | Pietro Di Lena [aut] (ORCID: <https://orcid.org/0000-0002-1838-8918>), Anna Plaksienko [aut, cre] (ORCID: <https://orcid.org/0000-0001-9607-057X>), Claudia Angelini [aut] (ORCID: <https://orcid.org/0000-0001-8350-8464>), Christine Nardini [aut] (ORCID: <https://orcid.org/0000-0001-7601-321X>) |
| License | GPL-3 |
| URL | https://github.com/annaplaksienko/methyLImp2 |
| Bug Reports | https://github.com/annaplaksienko/methyLImp2/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DNAMethylation, MethylationArray, Microarray, Regression, Software |
| Package Short Url | https://bioconductor.org/packages/methyLImp2/ |
Citation
From within R, enter citation("methyLImp2"):
Pietro Di Lena, Anna Plaksienko, Claudia Angelini, Christine Nardini. methyLImp2: Missing value estimation of DNA methylation data. doi:10.18129/B9.bioc.methyLImp2, R package version 1.8.0, https://bioconductor.org/packages/methyLImp2.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the 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 (arm64) | methyLImp2_1.8.0.tgz |
| macOS binary (x86_64) | methyLImp2_1.8.0.tgz |
Dependencies
Depends: R (>= 4.3.0), ChAMPdata
Imports: BiocParallel, parallel, stats, methods, corpcor, SummarizedExperiment, utils
Suggests: BiocStyle, knitr, rmarkdown, spelling, testthat (>= 3.0.0)