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QuaternaryProd

Computes the Quaternary Dot Product Scoring Statistic for Signed and Unsigned Causal Graphs


Bioconductor version: Release (3.18)

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.

Author: Carl Tony Fakhry [cre, aut], Ping Chen [ths], Kourosh Zarringhalam [aut, ths]

Maintainer: Carl Tony Fakhry <cfakhry at cs.umb.edu>

Citation (from within R, enter citation("QuaternaryProd")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("QuaternaryProd")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("QuaternaryProd")
QuaternaryProdVignette PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews GeneExpression, GraphAndNetwork, Software, Transcription
Version 1.36.0
In Bioconductor since BioC 3.3 (R-3.3) (8 years)
License GPL (>=3)
Depends R (>= 3.2.0), Rcpp (>= 0.11.3), dplyr, yaml (>= 2.1.18)
Imports
System Requirements
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Suggests knitr
Linking To Rcpp
Enhances
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package QuaternaryProd_1.36.0.tar.gz
Windows Binary QuaternaryProd_1.36.0.zip
macOS Binary (x86_64) QuaternaryProd_1.36.0.tgz
macOS Binary (arm64) QuaternaryProd_1.36.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/QuaternaryProd
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/QuaternaryProd
Bioc Package Browser https://code.bioconductor.org/browse/QuaternaryProd/
Package Short Url https://bioconductor.org/packages/QuaternaryProd/
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