Package: methyLImp2 1.9.0

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_1.9.0.tar.gz
methyLImp2_1.9.0.zip(r-4.7)methyLImp2_1.9.0.zip(r-4.6)methyLImp2_1.9.0.zip(r-4.5)
methyLImp2_1.9.0.tgz(r-4.6-any)methyLImp2_1.9.0.tgz(r-4.5-any)
methyLImp2_1.9.0.tar.gz(r-4.7-any)methyLImp2_1.9.0.tar.gz(r-4.6-any)
methyLImp2_1.9.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
methyLImp2/json (API)

# Install 'methyLImp2' in R:

install.packages('methyLImp2', repos = c('https://bioc.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)

dnamethylation microarray software methylationarray regression imputation methylation missing-value-imputation

5.42 score 8 stars 11 scripts 278 downloads 3 exports 28 dependencies

Last updated from:d5bec1036e. Checks:1 NOTE, 7 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	168
linux-devel-x86_64	WARNING	329
source / vignettes	OK	295
linux-release-x86_64	WARNING	312
macos-release-arm64	WARNING	197
macos-oldrel-arm64	WARNING	190
windows-devel	WARNING	276
windows-release	WARNING	313
windows-oldrel	WARNING	261
wasm-release	OK	156

Exports:evaluatePerformance generateMissingData methyLImp2

Dependencies:abind BH Biobase BiocGenerics BiocParallel ChAMPdata codetools corpcor cpp11 DelayedArray formatR futile.logger futile.options generics GenomicRanges IRanges lambda.r lattice Matrix MatrixGenerics matrixStats S4Arrays S4Vectors Seqinfo snow SparseArray SummarizedExperiment XVector

methyLImp2 vignette

Rendered frommethyLImp2_vignette.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
A subset of GSE199057 dataset for vignette demonstration	beta
An example of how custom (user provided) annotation data frame should look like	custom_anno_example
Evaluate performance metrics: root mean square error (RMSE), mean absolute error (MAE), mean absolute percentage error (MAPE) and Pearson correlation coefficient (PCC).	evaluatePerformance
Generation of artificial missing values	generateMissingData
Impute missing values in methylation dataset	methyLImp2