PROPS-package: PRObabilistic Pathway Score (PROPS)

In lhan22/PROPS: PRObabilistic Pathway Score (PROPS)

Description

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.

Details

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Calculates PRObabilistic Pathway Scores (PROPS), which are pathway-based features, from gene-based data.

Author(s)

Lichy Han

Maintainer: Lichy Han <[e-mail]>

References

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.

Examples

#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)

lhan22/PROPS documentation built on May 10, 2019, 1:17 p.m.