GRAPE: Gene-Ranking Analysis of Pathway Expression

Gene-Ranking Analysis of Pathway Expression (GRAPE) is a tool for summarizing the consensus behavior of biological pathways in the form of a template, and for quantifying the extent to which individual samples deviate from the template. GRAPE templates are based only on the relative rankings of the genes within the pathway and can be used for classification of tissue types or disease subtypes. GRAPE can be used to represent gene-expression samples as vectors of pathway scores, where each pathway score indicates the departure from a given collection of reference samples. The resulting pathway- space representation can be used as the feature set for various applications, including survival analysis and drug-response prediction. ---------------------------------------------------------------------------------------------- GRAPE is a generalization and extension of DIRAC, originally implemented in: Eddy, J.A., et al. (2010) <DOI:10.1371/journal.pcbi.1000792>. As a result, some of the software below may have been previously published in Matlab by the DIRAC authors and can be found at: https://price.systemsbiology.org/pricelab-resources/software/.

Author
Michael Klein <michael.klein@yale.edu>
Date of publication
2016-08-25 09:59:05
Maintainer
Michael Klein <michael.klein@yale.edu>
License
GPL-2
Version
0.1.0

View on CRAN

Man pages

getPathwayScores
Calculate Pathway Scores
makeBinaryTemplateAndProbabilityTemplate
Make binary template and probability template
makeGRAPE_psMat
Calculate Pathway Space Matrix
makePairwiseOrder
Make pairwise order representation of a sample
makePairwiseOrderNames
Make template names from gene names
predictClassDIRAC
DIRAC Classification
predictClassGRAPE
GRAPE Classification
predictClassPC
PC Classification
w_quad
Quadratic weight function

Files in this package

GRAPE
GRAPE/NAMESPACE
GRAPE/R
GRAPE/R/GRAPE_Pathway_Score_Functions.R
GRAPE/R/GRAPE_Basic_Functions.R
GRAPE/R/GRAPE_Classification_Functions.R
GRAPE/MD5
GRAPE/DESCRIPTION
GRAPE/man
GRAPE/man/getPathwayScores.Rd
GRAPE/man/predictClassPC.Rd
GRAPE/man/predictClassDIRAC.Rd
GRAPE/man/makeGRAPE_psMat.Rd
GRAPE/man/predictClassGRAPE.Rd
GRAPE/man/w_quad.Rd
GRAPE/man/makePairwiseOrder.Rd
GRAPE/man/makePairwiseOrderNames.Rd
GRAPE/man/makeBinaryTemplateAndProbabilityTemplate.Rd