lumi
Bioc currentBeadArray Specific Methods for Illumina Methylation and Expression Microarrays
Release Lineage
Entered 2.0 · Apr 26, 2007
Current · Requires R 4.6
Description
The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at the probe level. It also includes the functions of processing Illumina methylation microarrays, especially Illumina Infinium methylation microarrays.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
81 75 exported
Complexity
15.1 avg / 112 max
Call network
81 nodes / 78 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
11,817
Files
151
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
74
Internal functions
4
Testing
Has tests
No
Test-to-code ratio
0.00
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
14.3%
Unsafe pattern score
6
Dep constraint coverage
21.1%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
2.10
System requirements
–
C++ standard
–
License
LGPL (>= 2)
License flags
SPDX valid, OSI approved
History
Versions
39
First release
2007-04-24
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
28
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 88includes a package overview page
- Examples that run
- 90%64 run in a plain check · 7 hold no code
- Exported functions with examples
- 82%
- Documented parameters
- 98%
- Return-value docs
- 97%
- Help pages citing references
- 26%
Repository practices
Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.
No development-tooling practices detected in the Bioconductor git repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| example.lumi | – | – | – |
| example.lumiMethy | – | – | – |
| example.methyTitration | – | – | – |
Topics
Depended on by (16)
Show all 22 packagesHide all 22 packages
Bioconductor (16)
People (from the free-text Author field)
Cite
Cite this package
Run in R for the authors' entry:
citation("lumi")The package provides a citation file, so citation() returns the authors' own entry.
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.