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## try http:// if https:// URLs are not supported
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biocLite("QuaternaryProd")

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QuaternaryProd

DOI: 10.18129/B9.bioc.QuaternaryProd    

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

Bioconductor version: Release (3.5)

QuaternaryProd is an R package that performs causal reasoning on biological networks, including publicly available networks such as String-db. QuaternaryProd is a free alternative to commercial products such as Quiagen and 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. 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 String-db.

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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("QuaternaryProd")

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 1.4.0
In Bioconductor since BioC 3.3 (R-3.3) (1.5 years)
License GPL (>=3)
Depends R (>= 3.2.0), Rcpp (>= 0.11.3)
Imports
LinkingTo Rcpp
Suggests readr, org.Hs.eg.db, dplyr, stringr, knitr, fdrtool
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source QuaternaryProd_1.4.0.tar.gz
Windows Binary QuaternaryProd_1.4.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) QuaternaryProd_1.4.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/QuaternaryProd
Package Short Url http://bioconductor.org/packages/QuaternaryProd/
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