QuaternaryProd is an R package that performs causal reasoning on biological networks, including publicly available networks such as Stringdb. 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 Stringdb.
Author  Carl Tony Fakhry [cre, aut], Ping Chen [ths], Kourosh Zarringhalam [aut, ths] 
Bioconductor views  GeneExpression GraphAndNetwork Transcription 
Date of publication  None 
Maintainer  Carl Tony Fakhry <cfakhry@cs.umb.edu> 
License  GPL (>=3) 
Version  1.4.0 
Package repository  View on Bioconductor 
Installation  Install the latest version of this package by entering the following in R:



All man pages Function index File listing
Man pages  

BioQCREtoNet: Compute the Quaternary Dot Product Scoring Statistic for a...  
QP_Pmf: Computes the probability mass function of the scores.  
QP_Probability: Computes the probability of a score.  
QP_Pvalue: Computes the pvalue of a score.  
QP_SigPvalue: Computes the pvalue for a statistically significant score.  
QP_Support: Computes the support for the scores.  
QuaternaryProdpackage: Computes the Quaternary Dot Product Scoring Statistic for... 
Functions  

BioQCREtoNet  Man page Source code 
Pvalue_4by3  Source code 
QP_Pmf  Man page Source code 
QP_Probability  Man page Source code 
QP_Pvalue  Man page Source code 
QP_SigPvalue  Man page Source code 
QP_Support  Man page Source code 
QuaternaryProd  Man page 
QuaternaryProdpackage  Man page 
SigPvalue_4by3  Source code 
domain_4by3  Source code 
getGeneVals  Source code 
pmf_4by3  Source code 
runCRE  Source code 
user_probability_of_score_4by3  Source code 
Files  

DESCRIPTION
 
NAMESPACE
 
QuaternaryProd.Rproj
 
R
 
R/ProcessData.R  
R/RcppExports.R  
R/UserFunctions.R  
R/help.R  
build
 
build/vignette.rds
 
inst
 
inst/CITATION
 
inst/NEWS
 
inst/doc
 
inst/doc/QuaternaryProdVignette.R  
inst/doc/QuaternaryProdVignette.Rmd  
inst/doc/QuaternaryProdVignette.pdf
 
inst/extdata
 
inst/extdata/9606.protein.actions.v10.txt.gz
 
inst/extdata/e2f3_sig.txt
 
inst/extdata/myc_sig.txt
 
inst/extdata/ras_sig.txt
 
man
 
man/BioQCREtoNet.Rd  
man/QP_Pmf.Rd  
man/QP_Probability.Rd  
man/QP_Pvalue.Rd  
man/QP_SigPvalue.Rd  
man/QP_Support.Rd  
man/QuaternaryProdpackage.Rd  
src
 
src/QuaternaryProd.cpp
 
src/QuaternaryProd.h
 
src/QuaternaryProdUtils.cpp
 
src/QuaternaryProdUtils.h
 
src/RcppExports.cpp
 
vignettes
 
vignettes/QuaternaryProdVignette.Rmd 
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