methyLImp2

This is the development version of methyLImp2; for the stable release version, see methyLImp2.

Missing value estimation of DNA methylation data


Bioconductor version: Development (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 (from within R, enter citation("methyLImp2")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 PDF
NEWS Text

Details

biocViews DNAMethylation, MethylationArray, Microarray, Regression, Software
Version 1.1.1
In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)
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
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Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package methyLImp2_1.1.1.tar.gz
Windows Binary (x86_64) methyLImp2_1.1.1.zip
macOS Binary (x86_64) methyLImp2_1.1.1.tgz
macOS Binary (arm64) methyLImp2_1.1.1.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