QuaternaryProd (version 1.0.2)
Computes the Quaternary Dot Product Scoring Statistic for Signed and Unsigned
Causal Graphs
Description
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.