To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("ClusterSignificance")

In most cases, you don't need to download the package archive at all.

ClusterSignificance

DOI: 10.18129/B9.bioc.ClusterSignificance    

This is the development version of ClusterSignificance; for the stable release version, see ClusterSignificance.

The ClusterSignificance package provides tools to assess if class clusters in dimensionality reduced data representations have a separation different from permuted data

Bioconductor version: Development (3.6)

The ClusterSignificance package provides tools to assess if class clusters in dimensionality reduced data representations have a separation different from permuted data. The term class clusters here refers to, clusters of points representing known classes in the data. This is particularly useful to determine if a subset of the variables, e.g. genes in a specific pathway, alone can separate samples into these established classes. ClusterSignificance accomplishes this by, projecting all points onto a one dimensional line. Cluster separations are then scored and the probability of the seen separation being due to chance is evaluated using a permutation method.

Author: Jason T. Serviss and Jesper R. Gadin

Maintainer: Jason T Serviss <jason.serviss at ki.se>

Citation (from within R, enter citation("ClusterSignificance")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("ClusterSignificance")

Documentation

HTML R Script ClusterSignificance Vignette
PDF   Reference Manual
Text   NEWS

Details

biocViews Classification, Clustering, PrincipalComponent, Software, StatisticalMethod
Version 1.5.3
In Bioconductor since BioC 3.3 (R-3.3) (1.5 years)
License GPL-3
Depends R (>= 3.3.0)
Imports methods, pracma, princurve, scatterplot3d, RColorBrewer, grDevices, graphics, utils, stats
LinkingTo
Suggests knitr, rmarkdown, testthat, BiocStyle, ggplot2, plsgenomics
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package ClusterSignificance_1.5.3.tar.gz
Windows Binary ClusterSignificance_1.5.3.zip
Mac OS X 10.11 (El Capitan) ClusterSignificance_1.5.3.tgz
Source Repository git clone https://git.bioconductor.org/packages/ClusterSignificance
Package Short Url http://bioconductor.org/packages/ClusterSignificance/
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