R Observatory: Metrics for methyLImp2 version 1.8.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

methyLImp2

Bioc current

Missing value estimation of DNA methylation data

v1.8.0 · software · GPL-3

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.19 · May 1, 2024

Current · Requires R 4.6

1.0 In 5 of 49 releases 3.23

Description

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.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

9 3 exported

Complexity

7.2 avg / 31 max

Call network

9 nodes / 6 edges

Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.

Call graph

Open call graph →

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Lowest coverage

Per-function coverage is not measured for this package yet.

Code

Structure

Lines of code

1,251

Files

28

Compiled share

0%

Has compiled src

No

Language breakdown

R 781 (62.4%)Tests 119 (9.5%)Docs 229 (18.3%)Vignettes 122 (9.8%)

API

Exported functions

3

Internal functions

6

Recent export changes

v3.19+3 evaluatePerformance, generateMissingData, methyLImp2

Testing & CI

Has tests

Yes

Test-to-code ratio

0.15

testthat edition

3

CI present

No

CI type

[]

PR gated

No

Docs

Roxygen coverage

100%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

–

Unsafe pattern score

0

Dep constraint coverage

0%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

4.3.0

System requirements

–

C++ standard

–

License

GPL-3

License flags

SPDX valid, OSI approved

History

Versions

5

First release

2024-04-30

Latest release

2026-04-28

Avg cadence

182 days

Cold removal rate

–

Dep drift

0

LOC over versions

Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.

Documentation

READMEYes · 78 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 0% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Topics

Software › AssayDomain › DNAMethylation

Software › Technology › Microarray

Software

Software › Technology › Microarray › MethylationArray

Software › StatisticalMethod › Regression

People

Anna Plaksienko author maintainer
Claudia Angelini author
Pietro Di Lena author
Christine Nardini author

At a glance

Version: 1.8.0
Category: software
License: GPL-3
Requires R: ≥ 4.6
Maintainer: Anna Plaksienko
Entered: 3.19 · May 1, 2024
Current: 3.23 · Apr 29, 2026

Available on

CRAN r2u Bioconductor autoCRAN COPR

Dependencies

Depends

R (>= 4.3.0)ChAMPdataBioc

Imports

BiocParallelBiocparallelstatsmethodscorpcorSummarizedExperimentBiocutils

Suggests

BiocStyleBiocknitr rmarkdown spelling testthat (>= 3.0.0)

Source & history

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("methyLImp2")

Format

Plaksienko, A., Angelini, C., Di Lena, P., & Nardini, C. (2026). methyLImp2: Missing value estimation of DNA methylation data (Version 1.8.0) [Computer software]. https://bioconductor.org/packages/methyLImp2

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for methyLImp2 version 1.8.0 [Data set]. HJJB, LLC. Data release v2026-08-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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