QuaternaryProd
Computes the Quaternary Dot Product Scoring Statistic for Signed and Unsigned Causal Graphs
Bioconductor version: 3.24 · Package version: 1.47.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
QuaternaryProd is an R package that performs causal reasoning on biological networks, including publicly available networks such as STRINGdb. QuaternaryProd is an open-source alternative to commercial products such as Inginuity Pathway Analysis. For a given a set of differentially expressed genes, QuaternaryProd computes the significance of upstream regulators in the network by performing causal reasoning using the Quaternary Dot Product Scoring Statistic (Quaternary Statistic), Ternary Dot product Scoring Statistic (Ternary Statistic) and Fisher's exact test (Enrichment test). The Quaternary Statistic handles signed, unsigned and ambiguous edges in the network. Ambiguity arises when the direction of causality is unknown, or when the source node (e.g., a protein) has edges with conflicting signs for the same target gene. On the other hand, the Ternary Statistic provides causal reasoning using the signed and unambiguous edges only. The Vignette provides more details on the Quaternary Statistic and illustrates an example of how to perform causal reasoning using STRINGdb.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("QuaternaryProd")Details
| Maintainer | Carl Tony Fakhry <cfakhry@cs.umb.edu> |
| Author | Carl Tony Fakhry [cre, aut], Ping Chen [ths], Kourosh Zarringhalam [aut, ths] |
| License | GPL (>=3) |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | GeneExpression, GraphAndNetwork, Software, Transcription |
| Package Short Url | https://bioconductor.org/packages/QuaternaryProd/ |
Citation
From within R, enter citation("QuaternaryProd"):
Carl Tony Fakhry, Kourosh Zarringhalam. QuaternaryProd: Computes the Quaternary Dot Product Scoring Statistic for Signed and Unsigned Causal Graphs. doi:10.18129/B9.bioc.QuaternaryProd, R package version 1.47.0, https://bioconductor.org/packages/QuaternaryProd.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | QuaternaryProd_1.47.0.tar.gz |
| Windows binary (x86_64) | QuaternaryProd_1.47.0.zip |
| macOS binary (arm64) | QuaternaryProd_1.47.0.tgz |
| macOS binary (x86_64) | QuaternaryProd_1.47.0.tgz |
Dependencies
Depends: R (>= 3.2.0), Rcpp (>= 0.11.3), dplyr, yaml (>= 2.1.18)
LinkingTo: Rcpp
Suggests: knitr