Package: QuaternaryProd
Type: Package
Title: Computes the Quaternary Dot Product Scoring Statistic for Signed
        and Unsigned Causal Graphs
Version: 1.6.0
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-sorce 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 STRINGdb. 
License: GPL (>=3)
biocViews: GraphAndNetwork, GeneExpression, Transcription
Depends: R (>= 3.2.0), Rcpp (>= 0.11.3), dplyr, rlist
Suggests: knitr
LinkingTo: Rcpp
LazyData: true
VignetteBuilder: knitr
RoxygenNote: 6.0.1
NeedsCompilation: yes
Packaged: 2017-10-31 00:41:59 UTC; biocbuild
Author: Carl Tony Fakhry [cre, aut],
  Ping Chen [ths],
  Kourosh Zarringhalam [aut, ths]
Maintainer: Carl Tony Fakhry <cfakhry@cs.umb.edu>
Built: R 3.4.1; x86_64-pc-linux-gnu; 2018-02-16 09:19:16 UTC; unix
