Package: methyLImp2 1.8.0

Anna Plaksienko

methyLImp2: Missing value estimation of DNA methylation data

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.

Authors:Pietro Di Lena [aut], Anna Plaksienko [aut, cre], Claudia Angelini [aut], Christine Nardini [aut]

methyLImp2_1.8.0.tar.gz
methyLImp2_1.8.0.zip(r-4.7)methyLImp2_1.8.0.zip(r-4.6)methyLImp2_1.8.0.zip(r-4.5)
methyLImp2_1.8.0.tgz(r-4.6-any)methyLImp2_1.8.0.tgz(r-4.5-any)
methyLImp2_1.8.0.tar.gz(r-4.7-any)methyLImp2_1.8.0.tar.gz(r-4.6-any)
methyLImp2_1.8.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
methyLImp2/json (API)
NEWS

# Install 'methyLImp2' in R:
install.packages('methyLImp2', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/annaplaksienko/methylimp2/issues

Datasets:
  • beta - A subset of GSE199057 dataset for vignette demonstration
  • custom_anno_example - An example of how custom (user provided) annotation data frame should look like

On BioConductor:methyLImp2-1.9.0(bioc 3.24)methyLImp2-1.8.0(bioc 3.23)

dnamethylationmicroarraysoftwaremethylationarrayregressionimputationmethylationmissing-value-imputation

5.49 score 8 stars 13 scripts 278 downloads 3 exports 28 dependencies

Last updated from:49f40ee0e7 (on RELEASE_3_23). Checks:1 NOTE, 7 WARNING, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE197
linux-devel-x86_64WARNING358
source / vignettesOK282
linux-release-x86_64WARNING325
macos-release-arm64WARNING179
macos-oldrel-arm64WARNING227
windows-develWARNING229
windows-releaseWARNING256
windows-oldrelWARNING242
wasm-releaseOK172

Exports:evaluatePerformancegenerateMissingDatamethyLImp2

Dependencies:abindBHBiobaseBiocGenericsBiocParallelChAMPdatacodetoolscorpcorcpp11DelayedArrayformatRfutile.loggerfutile.optionsgenericsGenomicRangesIRangeslambda.rlatticeMatrixMatrixGenericsmatrixStatsS4ArraysS4VectorsSeqinfosnowSparseArraySummarizedExperimentXVector

methyLImp2 vignette

Anna Plaksienko

Rendered frommethyLImp2_vignette.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2024-09-09
Started: 2023-03-01