SETPath: Spiked Eigenvalue Test for Pathway data
Version 1.0

Tests gene expression data from a biological pathway for biologically meaningful differences in the eigenstructure between two classes. Specifically, it tests the null hypothesis that the two classes' leading eigenvalues and sums of eigenvalues are equal. A pathway's leading eigenvalue arguably represents the total variability due to variability in pathway activity, while the sum of all its eigenvalues represents the variability due to pathway activity and to other, unregulated causes. Implementation of the method described in Danaher (2015), "Covariance-based analyses of biological pathways".

AuthorPatrick Danaher
Date of publication2015-02-02 22:37:42
MaintainerPatrick Danaher <patrickjdanaher@gmail.com>
LicenseGPL-2
Version1.0
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("SETPath")

Getting started

Package overview

Popular man pages

d1: Example data for the SETPath method - dataset from class 1
d2: Example data for the SETPath method - dataset from class 2
pathwaynames: Names of the pathways used in the example.
setpath: Runs the Spiked Eigenvalue Test for Pathway data (SETPath) on...
SETPath-package: Spiked Eigenvalue Test for Pathway data
setpath.wrapper: Runs the Spiked Eigenvalue Test for Pathway data (SETPath) on...
unbias.eigens: Unbiased estimation of leading eigenvalues
See all...

All man pages Function index File listing

Man pages

d1: Example data for the SETPath method - dataset from class 1
d2: Example data for the SETPath method - dataset from class 2
pathwaygenes: Defines the gene memberships of the pathways in the example...
pathwaynames: Names of the pathways used in the example.
setpath: Runs the Spiked Eigenvalue Test for Pathway data (SETPath) on...
setpath.data: Example data for the SETPath method
SETPath-package: Spiked Eigenvalue Test for Pathway data
setpath.wrapper: Runs the Spiked Eigenvalue Test for Pathway data (SETPath) on...
unbias.eigens: Unbiased estimation of leading eigenvalues

Functions

SETPath Man page
SETPath-package Man page
d1 Man page
d2 Man page
pathwaygenes Man page
pathwaynames Man page
setpath Man page Source code
setpath.data Man page
setpath.wrapper Man page Source code
unbias.eigens Man page Source code

Files

NAMESPACE
data
data/setpath.data.rda
R
R/unbias.eigens.R
R/setpath.R
R/setpath.wrapper.R
MD5
DESCRIPTION
man
man/pathwaygenes.Rd
man/SETPath-package.Rd
man/d1.Rd
man/d2.Rd
man/setpath.data.Rd
man/pathwaynames.Rd
man/setpath.wrapper.Rd
man/unbias.eigens.Rd
man/setpath.Rd
SETPath documentation built on May 19, 2017, 9:07 p.m.

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