Package: methyLImp2 1.3.0

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_1.3.0.tar.gz
methyLImp2_1.3.0.zip(r-4.5)methyLImp2_1.3.0.zip(r-4.4)methyLImp2_1.3.0.zip(r-4.3)
methyLImp2_1.3.0.tgz(r-4.4-any)methyLImp2_1.3.0.tgz(r-4.3-any)
methyLImp2_1.3.0.tar.gz(r-4.5-noble)methyLImp2_1.3.0.tar.gz(r-4.4-noble)
methyLImp2_1.3.0.tgz(r-4.4-emscripten)methyLImp2_1.3.0.tgz(r-4.3-emscripten)
methyLImp2.pdf |methyLImp2.html✨
methyLImp2/json (API)
NEWS

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

Peer review:

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

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

On BioConductor:methyLImp2-1.3.0(bioc 3.21)methyLImp2-1.2.0(bioc 3.20)

dnamethylationmicroarraysoftwaremethylationarrayregressionimputationmethylationmissing-value-imputation

5.62 score 6 stars 3 scripts 126 downloads 3 exports 40 dependencies

Last updated 2 months agofrom:613be1fffc. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 18 2024
R-4.5-winNOTEDec 18 2024
R-4.5-linuxNOTEDec 18 2024
R-4.4-winNOTEDec 18 2024
R-4.4-macNOTEDec 18 2024
R-4.3-winNOTEDec 18 2024
R-4.3-macNOTEDec 18 2024

Exports:evaluatePerformancegenerateMissingDatamethyLImp2

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocParallelChAMPdatacodetoolscorpcorcpp11crayoncurlDelayedArrayformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesjsonlitelambda.rlatticeMatrixMatrixGenericsmatrixStatsmimeopensslR6S4ArraysS4VectorssnowSparseArraySummarizedExperimentsysUCSC.utilsXVectorzlibbioc

methyLImp2 vignette

Anna Plaksienko

Rendered frommethyLImp2_vignette.Rmdusingknitr::rmarkdownon Dec 18 2024.

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