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

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("QuaternaryProd")
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)
Version1.2.0

View on Bioconductor

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

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