methylumi
Bioc currentHandle Illumina methylation data
Release Lineage
Entered 2.5 · Oct 28, 2009
Current · Requires R 4.6
Description
This package provides classes for holding and manipulating Illumina methylation data. Based on eSet, it can contain MIAME information, sample information, feature information, and multiple matrices of data. An "intelligent" import function, methylumiR can read the Illumina text files and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from HumanMethylation27 and HumanMethylation450 microarrays. Normalization, background correction, and quality control features for GoldenGate, Infinium, and Infinium HD arrays are also included.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
98 29 exported
Complexity
3.9 avg / 24 max
Call network
98 nodes / 71 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
6,966
Files
71
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
30
Internal functions
54
Testing
Has tests
Yes
Test-to-code ratio
0.08
testthat edition
3
Docs
Roxygen coverage
96.7%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
12.5%
Unsafe pattern score
3
Dep constraint coverage
3.6%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.0
System requirements
–
C++ standard
–
License
GPL-2
License flags
SPDX valid, OSI approved
History
Versions
34
First release
2009-10-27
Latest release
2026-08-14
Avg cadence
184 days
Cold removal rate
100%
Dep drift
24
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 24includes a package overview page
- Examples that run
- 93%14 run in a plain check · 1 never run
- Exported functions with examples
- 45%
- Documented parameters
- 92%
- Return-value docs
- 64%
- Help pages citing references
- 17%
- methylumi.html HTML
- methylumi450k.html HTML
Repository practices
5 development-tooling and community-health practices detected across 2 families in the upstream repository
Checks run against github.com/seandavi/methylumi on 2026-10-11.
The R CMD check workflow runs on Linux, and on R-devel
GitHub Pages site last deployed 2026-08-14 · The repository has a site deploy workflow
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| CpGs | data.frame | 487,177 × 5 | No other package |
| exampledata.controls | data.frame | 44 × 52 | No other package |
| exampledata.samples | – | – | – |
| mldat | – | – | – |
| samples | data.frame | 10 × 4 | No other package |
| substitutions | data.frame | 8 × 2 | No other package |
Topics
Depended on by (8)
Bioconductor (8)
People (from the free-text Author field)
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("methylumi")Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.