BEclear
Bioc currentCorrection of batch effects in DNA methylation data
Release Lineage
Entered 3.1 · Apr 17, 2015
Current · Requires R 4.6
Description
Provides functions to detect and correct for batch effects in DNA methylation data. The core function is based on latent factor models and can also be used to predict missing values in any other matrix containing real numbers.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
23 13 exported
Complexity
5.4 avg / 32 max
Call network
23 nodes / 17 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
4,271
Files
75
Compiled share
1.6%
Has compiled src
Yes
Language breakdown
API
Exported functions
13
Internal functions
6
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.25
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
15.4%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
–
System requirements
1 externalC++11
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
23
First release
2015-04-16
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
17
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 24 (8 internal)includes a package overview page
- Examples that run
- 100%12 run in a plain check
- Exported functions with examples
- 85%
- Documented parameters
- 92%
- Return-value docs
- 100%
- Help pages citing references
- 29% with a bibliography file
- BEclear tutorial HTML
Repository practices
2 development-tooling and community-health practices detected across 2 families in the upstream repository
Checks run against github.com/uds-helms/beclear on 2026-10-11.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| ex.corrected.data | data.frame | 250 × 40 | No other package |
| ex.data | matrix | 250 × 40 | No other package |
| ex.samples | data.frame | 40 × 2 | No other package |
Topics
People
- Livia Rasp author maintainer
- Ruslan Akulenko author
- Markus Merl author
Cite
Cite this package
Run in R for the authors' entry:
citation("BEclear")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1371/journal.pone.0159921.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.