pcaMethods
Bioc currentA collection of PCA methods
Release Lineage
Entered 1.9 · Oct 4, 2006
Current · Requires R 4.6
Description
Provides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method for missing value estimation is included for comparison. BPCA, PPCA and NipalsPCA may be used to perform PCA on incomplete data as well as for accurate missing value estimation. A set of methods for printing and plotting the results is also provided. All PCA methods make use of the same data structure (pcaRes) to provide a common interface to the PCA results. Initiated at the Max-Planck Institute for Molecular Plant Physiology, Golm, Germany.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
52 23 exported
Complexity
7.8 avg / 35 max
Call network
52 nodes / 47 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
9,170
Files
123
Compiled share
2.2%
Has compiled src
Yes
Language breakdown
API
Exported functions
23
Internal functions
25
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
0%
Unsafe pattern score
18
Dep constraint coverage
20%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
–
System requirements
1 externalRcpp
C++ standard
–
License
GPL (>= 3)
License flags
SPDX valid, OSI approved
History
Versions
40
First release
2007-04-19
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
88.9%
Dep drift
5
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 80includes a package overview page
- Examples that run
- 100%28 run in a plain check
- Exported functions with examples
- 78%
- Documented parameters
- 99%
- Return-value docs
- 100%
- Help pages citing references
- 18%
Repository practices
Checks run against github.com/hredestig/pcamethods on 2026-10-22.
No development-tooling practices detected in the upstream repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| helix | matrix | 1,000 × 3 | No other package |
| metaboliteData | matrix | 154 × 52 | No other package |
| metaboliteDataComplete | matrix | 154 × 52 | No other package |
Topics
Depended on by (35)
Show all 44 packagesHide all 44 packages
Bioconductor (19)
CRAN (16)
Suggested by (9)
People
- Henning Redestig author maintainer
- Wolfram Stacklies author
- Kevin Wright author
Cite
Cite this package
Run in R for the authors' entry:
citation("pcaMethods")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 v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.