SourceSet v0.1.1

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A Graphical Model Approach to Identify Primary Genes in Perturbed Biological Pathways

The algorithm pursues the identification of the set of variables driving the differences in two different experimental conditions (i.e., the primary genes) within a graphical model context. It uses the idea of simultaneously looking for the differences between two multivariate normal distributions in all marginal and conditional distributions associated with a decomposable graph, which represents the pathway under exam. The implementation accommodates genomics specific issues (low sample size and multiple testing issues) and provides a number of functions offering numerical and visual summaries to help the user interpret the obtained results. In order to use the (optional) 'Cytoscape' functionalities, the suggested 'r2cytoscape' package must be installed from the 'GitHub' repository ('devtools::install_github('cytoscape/r2cytoscape')').

Functions in SourceSet

Name Description
shrinkTEGS Default shrinkage estimation of covariance matrices
ripAllRootsClique All possible RIP orderings
easyLookSource Easy look results
sourceCytoscape Visualize in Cytoscape a collection of graphs analyzed with the source set algorithm
parameters Estimation of parameters for test equality of two normal distributions
simulation Simulated dataset
infoSource Get summary statistics on graphs and variables
getPermutations Get random permutations of a set of elements
sourceSankeyDiagram Create a D3 JavaScript Sankey diagram
testMeanVariance Test the equality of two normal distributions
sourceUnionCytoscape Visualize in Cytoscape the graphical union induced by the source sets of a collection of graphs
sourceSet Source Set
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Vignettes of SourceSet

Name
images/CytoALL.png
images/CytoSimulation.png
images/RunTime.png
images/RunTimeSimulation.png
SourceSet.Rmd
bibliography.bib
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Details

Type Package
Date 2018-04-23
License AGPL-3
Encoding UTF-8
LazyData true
RoxygenNote 6.0.1
VignetteBuilder knitr
NeedsCompilation no
Packaged 2018-04-23 16:11:27 UTC; Elisetta
Repository CRAN
Date/Publication 2018-04-24 08:00:41 UTC

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