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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). The package is based on the method described in Massa M.S., Chiogna M., Romualdi C. (2010) <doi:10.1186/1752-0509-4-121>.
| Version: | 1.5.0 |
| Imports: | graph, gRbase (≥ 2.0), qpgraph, fields, methods, igraph |
| Suggests: | Rgraphviz |
| Published: | 2023-09-25 |
| DOI: | 10.32614/CRAN.package.topologyGSA |
| Author: | Sofia Massa, Gabriele Sales |
| Maintainer: | Gabriele Sales <gabriele.sales at unipd.it> |
| License: | GPL-3 |
| NeedsCompilation: | no |
| In views: | Omics |
| CRAN checks: | topologyGSA results |
| Reference manual: | topologyGSA.pdf |
| Package source: | topologyGSA_1.5.0.tar.gz |
| Windows binaries: | r-devel: topologyGSA_1.5.0.zip, r-release: topologyGSA_1.5.0.zip, r-oldrel: topologyGSA_1.5.0.zip |
| macOS binaries: | r-release (arm64): topologyGSA_1.5.0.tgz, r-oldrel (arm64): topologyGSA_1.5.0.tgz, r-release (x86_64): topologyGSA_1.5.0.tgz, r-oldrel (x86_64): topologyGSA_1.5.0.tgz |
| Old sources: | topologyGSA archive |
| Reverse suggests: | graphite |
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