R Observatory: Metrics for LumiWCluster version 1.0.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2014-05-01. Its history is shown below.

Reason: memory-access errors were not corrected

Details below reflect version 1.0.2, its last release before removal.

LumiWCluster

1.0.2

Weighted model based clustering

0packages depend

–downloads / year

–test coverage

–checks pass

Overview

About

Maintained by Xin Zhou1 releasesCRAN page ↗

The LumiWCluster package implements the proposed weighted model based clustering for Illumina Methylation BeadArray (Kuan et al., 2010). There are two parts to this package. The first part provides function to normalize the methylation data from the Illumina GoldenGate platform. We will include the normalization for Illumina Infinium platform in future. The second part provides function to identify subgroups with distinct methylation profiles in Illumina BeadArray. It works for both Infinium and GoldenGate platform, as well as any other platforms including gene expression arrays. The core of the algorithm is based on the paper by Wang and Zhu (2008), which automatically selects important CpGs/probes. LumiWCluster incorporates the detection p-values (a quality measure of probe performance reported by Illumina BeadStudio or GenomeStudio) systematically in the clustering algorithm and avoids arbitrary cutoff for excluding unreliable probes. Further details and motivation can be found in Kuan et al. (2010).

Install

R (source archive)

url <- "https://cran.r-project.org/src/contrib/Archive/LumiWCluster/LumiWCluster_1.0.2.tar.gz"
pkgFile <- "LumiWCluster_1.0.2.tar.gz"
download.file(url, pkgFile)
install.packages(pkgFile, type = "source", repos = NULL)

This package is no longer on CRAN, so install.packages() cannot fetch it by name. This downloads the last archived source (1.0.2) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

Health

CRAN checks

CRAN check results are not tracked yet.

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

0

Dependencies · direct

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 97%
Return-value docs: 100%
References docs: 100%

Downloads

LumiWCluster Releases R versions

Daily download trend is not available in this view yet.

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Dependencies

Declared dependencies

0 external dependencies (excludes base and recommended)

Depends (1)

R >= 2.10.0

Imports (0)

none

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (2)

Other (2)

Pei Fen Kuan

Contributor

Xin Zhou

Contributor

Package Timeline

1 release. R releases are shown for context.

R
R 3.2.0 released · 2015-04-16
archivedRemoved from CRAN
2014-05-01
memory-access errors were not corrected
R
R 3.1.0 released · 2014-04-10
R
R 3.0.0 released · 2013-04-03
R
R 2.15.0 released · 2012-03-30
R
R 2.14.0 released · 2011-10-31
R
R 2.13.0 released · 2011-04-13
R
R 2.12.0 released · 2010-10-15
1.0.2
2010-09-02
R
R 2.11.0 released · 2010-04-22

Package metadata

Total releases: 1
License: GPL (>= 2) OSI
Minimum R: ≥ 2.10.0
Bundled data: 156 KB / 3 files
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("LumiWCluster")

Format

Kuan, P. F., & Zhou, X. (n.d.). LumiWCluster: Weighted model based clustering (Version 1.0.2) [Computer software]. Retrieved August 13, 2026, from https://CRAN.R-project.org/package=LumiWCluster

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for LumiWCluster version 1.0.2 [Data set]. HJJB, LLC. Data release v2026-08-11. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-11, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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