| PROPS-package {PROPS} | R Documentation |
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:
| Package: | PROPS |
| Type: | Package |
| Title: | PRObabilistic Pathway Score (PROPS) |
| Version: | 1.4.0 |
| 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_8 |
| git_last_commit: | f4ca190 |
| git_last_commit_date: | 2018-10-30 |
| Date/Publication: | 2018-10-30 |
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.
Lichy Han
Maintainer: Lichy Han <lhan2@stanford.edu>
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.
#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)