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")
```

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 | 1.2.0 |

**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...

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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Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.

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