QuaternaryProd-package: 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.

Arguments

Details

Package:

QuaternaryProd

Type:

Package

Version:

0.99.6

Date:

2015-10-22

License:

GPL (>= 2)

References

C. T. Fakhry, P. Choudhary, A. Gutteridge, B. Sidders, P. Chen, D. Ziemek, K. Zarringhalam (2016). Interpreting transcriptional changes using causal graphs: new methods and their practical utility on public networks. submitted.

Franceschini, A (2013). STRING v9.1: protein-protein interaction networks, with increased coverage and integration. In:'Nucleic Acids Res. 2013 Jan;41(Database issue):D808-15. doi: 10.1093/nar/gks1094. Epub 2012 Nov 29'.