normalize450K
Bioc currentPreprocessing of Illumina Infinium 450K data
Release Lineage
Entered 3.3 · May 4, 2016
Current · Requires R 4.6
Description
Precise measurements are important for epigenome-wide studies investigating DNA methylation in whole blood samples, where effect sizes are expected to be small in magnitude. The 450K platform is often affected by batch effects and proper preprocessing is recommended. This package provides functions to read and normalize 450K '.idat' files. The normalization corrects for dye bias and biases related to signal intensity and methylation of probes using local regression. No adjustment for probe type bias is performed to avoid the trade-off of precision for accuracy of beta-values.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
4 4 exported
Complexity
3.5 avg / 7 max
Call network
4 nodes / 0 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
411
Files
12
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
4
Internal functions
0
Testing & CI
Has tests
No
Test-to-code ratio
0.00
testthat edition
–
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
3.3
System requirements
–
C++ standard
–
License
BSD_2_clause + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
21
First release
2016-05-03
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
- Examples that run
- 0%
- Documented parameters
- 100%
- Return-value docs
- 100%
- References docs
- 100%
Topics
People
Jonathan Alexander Heiss