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 |

**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...

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

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