QuaternaryProd

DOI: 10.18129/B9.bioc.QuaternaryProd    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see QuaternaryProd.

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

Bioconductor version: 3.8

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>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("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")

 

PDF	R Script	QuaternaryProdVignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneExpression, GraphAndNetwork, Software, Transcription
Version	1.16.0
In Bioconductor since	BioC 3.3 (R-3.3) (3 years)
License	GPL (>=3)
Depends	R (>= 3.2.0), Rcpp (>= 0.11.3), dplyr, yaml (>= 2.1.18)
Imports
LinkingTo	Rcpp
Suggests	knitr
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	QuaternaryProd_1.16.0.tar.gz
Windows Binary	QuaternaryProd_1.16.0.zip (64-bit only)
Mac OS X 10.11 (El Capitan)	QuaternaryProd_1.16.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/QuaternaryProd
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/QuaternaryProd
Package Short Url	http://bioconductor.org/packages/QuaternaryProd/
Package Downloads Report	Download Stats