Computes the Quaternary Dot Product Scoring Statistic for Signed
and Unsigned Causal Graphs // 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.