This package calculates probabilistic pathway scores using gene expression data. Gene expression values are aggregated into pathway-based scores using Bayesian network representations of biological pathways.
The DESCRIPTION file:
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Calculates PRObabilistic Pathway Scores (PROPS), which are pathway-based features, from gene-based data.
Maintainer: Lichy Han <firstname.lastname@example.org>
Lichy Han, Mateusz Maciejewski, Christoph Brockel, William Gordon, Scott B. Snapper, Joshua R. Korzenik, Lovisa Afzelius, Russ B. Altman. A PRObabilistic Pathway Score (PROPS) for Classification with Applications to Inflammatory Bowel Disease.
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#Load in randomly generated example data #Each row is a sample #Each column is a gene, named with Entrez Gene ID data(example_healthy) data(example_data) #Run PROPS with default KEGG pathway edges props_features <- props(example_healthy, example_data) #Run PROPS with user input edges data(example_edges) props_features2 <- props(example_healthy, example_data, example_edges)
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