# topologyGSA: Gene Set Analysis Exploiting Pathway Topology

Using Gaussian graphical models we propose a novel approach to perform pathway analysis using gene expression. Given the structure of a graph (a pathway) we introduce two statistical tests to compare the mean and the concentration matrices between two groups. Specifically, these tests can be performed on the graph and on its connected components (cliques).

- Author
- Sofia Massa, Gabriele Sales
- Date of publication
- 2016-09-22 16:51:06
- Maintainer
- Gabriele Sales <gabriele.sales@unipd.it>
- License
- GPL-3
- Version
- 1.4.6

## Man pages

- clique.mean.test
- Comparison of all the cliques of a pathway.
- clique.var.test
- Testing the concentration matrices of all cliques of a...
- dag_bcell
- DAG representation of the B cell receptor signaling pathway
- pathway.mean.test
- Testing the means of a pathway.
- pathway.var.test
- Testing the concentration matrices of a pathway.
- Print results of statistical tests.
- render.significant.cliques
- Graphical display of the significant cliques
- y1
- Gene expression signatures in acute lymphocytic leukemia for...
- y2
- Gene expression signatures in acute lymphocytic leukemia for...

## Files in this package

topologyGSA |

topologyGSA/COPYING |

topologyGSA/NAMESPACE |

topologyGSA/data |

topologyGSA/data/examples.RData |

topologyGSA/R |

topologyGSA/R/hote.R |

topologyGSA/R/multt.R |

topologyGSA/R/cov.R |

topologyGSA/R/render.R |

topologyGSA/R/cliques.R |

topologyGSA/R/graph.R |

topologyGSA/R/print.R |

topologyGSA/R/params.R |

topologyGSA/R/pathway.R |

topologyGSA/MD5 |

topologyGSA/DESCRIPTION |

topologyGSA/man |

topologyGSA/man/clique.mean.test.Rd |

topologyGSA/man/y2.Rd |

topologyGSA/man/clique.var.test.Rd |

topologyGSA/man/y1.Rd |

topologyGSA/man/pathway.var.test.Rd |

topologyGSA/man/render.significant.cliques.Rd |

topologyGSA/man/pathway.mean.test.Rd |

topologyGSA/man/print.Rd |

topologyGSA/man/dag_bcell.Rd |