# SourceSet v0.1.0

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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 infoSource Get summary statistics on graphs and variables parameters Estimation of parameters for test equality of two normal distributions simulation Simulated dataset sourceCytoscape Visualize in Cytoscape a collection of graphs analyzed with the source set algorithm sourceSankeyDiagram Create a D3 JavaScript Sankey diagram sourceSet Source Set ripAllRootsClique All possible RIP orderings shrinkTEGS Default shrinkage estimation of covariance matrices sourceUnionCytoscape Visualize in Cytoscape the graphical union induced by the source sets of a collection of graphs testMeanVariance Test the equality of two normal distributions easyLookSource Easy look results getPermutations Get random permutations of a set of elements No Results!

## Details

 Type Package Date 2018-02-27 License AGPL-3 Encoding UTF-8 LazyData true RoxygenNote 6.0.1 VignetteBuilder knitr NeedsCompilation no Packaged 2018-02-28 16:28:27 UTC; Elisetta Repository CRAN Date/Publication 2018-02-28 17:36:07 UTC
 suggests ALL , Biobase , BiocStyle , ggplot2 , graphite , grDevices , hgu95av2.db , knitr , mvtnorm , networkD3 , org.Hs.eg.db , r2cytoscape , Rgraphviz , rmarkdown imports graph , gRbase , gtools , igraph , methods , plyr , progress , reshape2 , scales depends R (>= 2.10) Contributors Chiara Romualdi, Monica Chiogna, Vera Djordjilovic