PROPS-package {PROPS} | R Documentation

## 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

The DESCRIPTION file:

Package: | PROPS
Type: | Package
Title: | PRObabilistic Pathway Score (PROPS)
Version: | 1.10.0
Date: | 2017-10-23
Author: | Lichy Han
Maintainer: | Lichy Han <lhan2@stanford.edu>
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.
License: | GPL-2
NeedsCompilation: | no
Imports: | bnlearn, reshape2, sva, stats, utils, Biobase
Suggests: | knitr, rmarkdown
VignetteBuilder: | knitr
biocViews: | Classification, Bayesian, GeneExpression
Packaged: | 2017-08-24 18:11:54 UTC; lichy
git_url: | https://git.bioconductor.org/packages/PROPS
git_branch: | RELEASE_3_11
git_last_commit: | 35f9762
git_last_commit_date: | 2020-04-27
Date/Publication: | 2020-04-27

Index of help topics:

    PROPS-package           PRObabilistic Pathway Score (PROPS)
    example_data            Example data, 50 samples, 22600 genes.
    example_edges           Example pathway edges. Contains 3 randomly
                            generated pathways.
    example_healthy         Example healthy data, 100 samples, 22600 genes.
    kegg_pathway_edges      KEGG pathway edges
    props                   PRObabilistic Pathway Scores (PROPS)

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

### Author(s)

Lichy Han

Maintainer: Lichy Han <lhan2@stanford.edu>

### 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)

[Package PROPS version 1.10.0 Index]