QuaternaryProd: Computes the Quaternary Dot Product Scoring Statistic for Signed and Unsigned Causal Graphs
Version 1.4.0

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.

AuthorCarl Tony Fakhry [cre, aut], Ping Chen [ths], Kourosh Zarringhalam [aut, ths]
Bioconductor views GeneExpression GraphAndNetwork Transcription
Date of publicationNone
MaintainerCarl Tony Fakhry <cfakhry@cs.umb.edu>
LicenseGPL (>=3)
Version1.4.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("QuaternaryProd")

Getting started

Package overview
QuaternaryProd

Popular 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 p-value of a score.
QP_SigPvalue: Computes the p-value for a statistically significant score.
QP_Support: Computes the support for the scores.
QuaternaryProd-package: Computes the Quaternary Dot Product Scoring Statistic for...
See all...

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 p-value of a score.
QP_SigPvalue: Computes the p-value for a statistically significant score.
QP_Support: Computes the support for the scores.
QuaternaryProd-package: 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
QuaternaryProd-package 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/QuaternaryProd-package.Rd
src
src/QuaternaryProd.cpp
src/QuaternaryProd.h
src/QuaternaryProdUtils.cpp
src/QuaternaryProdUtils.h
src/RcppExports.cpp
vignettes
vignettes/QuaternaryProdVignette.Rmd
QuaternaryProd documentation built on May 20, 2017, 9:38 p.m.

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