SETPath: Spiked Eigenvalue Test for Pathway data

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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".

Author
Patrick Danaher
Date of publication
2015-02-02 22:37:42
Maintainer
Patrick Danaher <patrickjdanaher@gmail.com>
License
GPL-2
Version
1.0

View on CRAN

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

Files in this package

SETPath
SETPath/NAMESPACE
SETPath/data
SETPath/data/setpath.data.rda
SETPath/R
SETPath/R/unbias.eigens.R
SETPath/R/setpath.R
SETPath/R/setpath.wrapper.R
SETPath/MD5
SETPath/DESCRIPTION
SETPath/man
SETPath/man/pathwaygenes.Rd
SETPath/man/SETPath-package.Rd
SETPath/man/d1.Rd
SETPath/man/d2.Rd
SETPath/man/setpath.data.Rd
SETPath/man/pathwaynames.Rd
SETPath/man/setpath.wrapper.Rd
SETPath/man/unbias.eigens.Rd
SETPath/man/setpath.Rd