Package: QuaternaryProd
Type: Package
Title: Computes the Quaternary Dot Product Scoring Statistic for Signed
        and Unsigned Causal Graphs
Version: 1.45.0
Date: 2015-10-22
Authors@R: c(
    person("Carl Tony", "Fakhry", email = "cfakhry@cs.umb.edu", role = c("cre","aut")),
    person("Ping", "Chen", role = "ths"),
    person("Kourosh", "Zarringhalam", role = c("aut","ths")))
Description: QuaternaryProd is an R package that performs causal
        reasoning on biological networks, including publicly available
        networks such as STRINGdb. QuaternaryProd is an open-source
        alternative to commercial products such as 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 (Enrichment 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
        STRINGdb.
License: GPL (>=3)
biocViews: GraphAndNetwork, GeneExpression, Transcription
Depends: R (>= 3.2.0), Rcpp (>= 0.11.3), dplyr, yaml (>= 2.1.18)
Suggests: knitr
LinkingTo: Rcpp
VignetteBuilder: knitr
RoxygenNote: 6.1.0
Encoding: UTF-8
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 14:29:19 UTC
RemoteUrl: https://github.com/bioc/QuaternaryProd
RemoteRef: HEAD
RemoteSha: 955c5f105adcc68060058f0d68c52c3d50b00dc8
NeedsCompilation: yes
Packaged: 2026-01-04 16:03:02 UTC; root
Author: Carl Tony Fakhry [cre, aut],
  Ping Chen [ths],
  Kourosh Zarringhalam [aut, ths]
Maintainer: Carl Tony Fakhry <cfakhry@cs.umb.edu>
Built: R 4.6.0; aarch64-apple-darwin23; 2026-01-04 16:05:34 UTC; unix
