Skip to content

affyPLM

Bioc current

Methods for fitting probe-level models

v1.88.0 · software · GPL (>= 2)
View on Bioconductor ↗ Source ↗

Release Lineage

Entered 1.4 · May 17, 2004

Current · Requires R 4.6

1.0 In 45 of 49 releases 3.23

Description

A package that extends and improves the functionality of the base affy package. Routines that make heavy use of compiled code for speed. Central focus is on implementation of methods for fitting probe-level models and tools using these models. PLM based quality assessment tools.

Code & tests

Open call graph →

Line coverage

–

Expression

–

Tests / Examples

–

Functions

190 0 exported

Complexity

10.3 avg / 103 max

Call network

190 nodes / 196 edges

Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.

Loading call graph…

Lowest coverage

Per-function coverage is not measured for this package yet.

Code

Structure

Lines of code

18,999

Files

114

Compiled share

58.3%

Has compiled src

Yes

Language breakdown

R 4,456 (23.5%)C/C++/src 11,084 (58.3%)Tests 1,258 (6.6%)Docs 916 (4.8%)Vignettes 1,285 (6.8%)

API

Exported functions

37

Internal functions

4

Testing & CI

Has tests

Yes

Test-to-code ratio

0.28

testthat edition

–

CI present

No

CI type

[]

PR gated

No

Docs

Return-value doc rate

–

\dontrun example ratio

0%

Roxygen coverage

–

Has pkgdown

No

NEWS present

No

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

0%

Unsafe pattern score

0

Dep constraint coverage

44.4%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

2.6.0

System requirements

–

C++ standard

–

License

GPL (>= 2)

License flags

SPDX valid, OSI approved

History

Versions

45

First release

2004-08-23

Latest release

2026-04-28

Avg cadence

183 days

Cold removal rate

–

Dep drift

13

LOC over versions

v1.4: 14,112 LOCv1.5: 15,541 LOCv1.6: 21,804 LOCv1.7: 21,821 LOCv1.8: 22,637 LOCv1.9: 24,995 LOCv2.0: 25,743 LOCv2.1: 20,535 LOCv2.2: 18,187 LOCv2.3: 18,202 LOCv2.4: 17,668 LOCv2.5: 17,704 LOCv2.6: 17,722 LOCv2.8: 17,723 LOCv2.7: 17,722 LOCv2.9: 17,723 LOCv2.10: 17,723 LOCv2.11: 17,718 LOCv2.12: 17,718 LOCv2.13: 17,718 LOCv2.14: 19,002 LOCv3.0: 19,001 LOCv3.1: 19,001 LOCv3.2: 19,001 LOCv3.3: 19,001 LOCv3.4: 19,000 LOCv3.5: 19,000 LOCv3.6: 19,000 LOCv3.7: 19,000 LOCv3.8: 19,000 LOCv3.9: 19,000 LOCv3.10: 19,000 LOCv3.11: 19,000 LOCv3.12: 19,000 LOCv3.13: 18,999 LOCv3.14: 18,999 LOCv3.15: 18,999 LOCv3.16: 18,999 LOCv3.17: 18,999 LOCv3.18: 18,999 LOCv3.19: 18,999 LOCv3.20: 18,999 LOCv3.21: 18,999 LOCv3.22: 18,999 LOCv3.23: 18,999 LOC

Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.

Topics

Software › Technology › Microarray
Software › Technology › Microarray › OneChannel
Software › WorkflowStep › Preprocessing
Software › WorkflowStep › QualityControl

Depended on by (18)

Bioconductor (16)

affylmGUI arrayMvout arrayQualityMetrics BiocGenerics frmaTools metahdep mimager piano AffyExpress affyQCReport ArrayTools BiocCaseStudies BiocGenerics_test BiocGenerics_test_two ELBOW RefPlus

CRAN (2)

bapred aroma.affymetrix

People

Ben Bolstad