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: 1.2.0
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

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 1.2.0 Index]