QuaternaryProd-package: Computes the Quaternary Dot Product Scoring Statistic for...
In QuaternaryProd: Computes the Quaternary Dot Product Scoring Statistic for Signed and Unsigned Causal Graphs
Description
Details
Author(s)
References
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.
Details
Package: QuaternaryProd
Type: Package
Version: 1.15.3
Date: 2015-10-22
License: GPL (>= 2)
Author(s)
Carl Tony Fakhry, Ping Chen and Kourosh Zarringhalam
Maintainer: Carl Tony Fakhry <cfakhry@cs.umb.edu>
References
Carl Tony Fakhry, Parul Choudhary, Alex Gutteridge, Ben Sidders, Ping Chen, Daniel Ziemek, and Kourosh Zarringhalam. Interpreting transcriptional changes using causal graphs: new methods and their practical utility on public networks. BMC Bioinformatics, 17:318, 2016. ISSN 1471-2105. doi: 10.1186/s12859-016-1181-8.
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'.
QuaternaryProd documentation built on Nov. 8, 2020, 8:23 p.m.
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Description Details Author(s) References
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.
Details
| Package: | QuaternaryProd |
| Type: | Package |
| Version: | 1.15.3 |
| Date: | 2015-10-22 |
| License: | GPL (>= 2) |
Author(s)
Carl Tony Fakhry, Ping Chen and Kourosh Zarringhalam
Maintainer: Carl Tony Fakhry <cfakhry@cs.umb.edu>
References
Carl Tony Fakhry, Parul Choudhary, Alex Gutteridge, Ben Sidders, Ping Chen, Daniel Ziemek, and Kourosh Zarringhalam. Interpreting transcriptional changes using causal graphs: new methods and their practical utility on public networks. BMC Bioinformatics, 17:318, 2016. ISSN 1471-2105. doi: 10.1186/s12859-016-1181-8.
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'.
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