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

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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]
Date of publication
None
Maintainer
Carl Tony Fakhry <cfakhry@cs.umb.edu>
License
GPL (>=3)
Version
1.2.0

View on Bioconductor

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...

Files in this package

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