QP_Support

Expected number of regulated predictions.

Number of positive predictions from experiments.

Number of negative predictions from experiments.

Number of nil predictions from experiments.


This function computes the support of the Quaternary Dot Product Scoring distribution
for signed causal graphs. This includes all scores which have probabilities strictly greater than 0.


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.

Carl Tony Fakhry

QuaternaryProd

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

QP_Support function

This function computes the support of the Quaternary Dot Product Scoring distribution
for signed causal graphs. This includes all scores which have probabilities strictly greater than 0.

QP_Support: Computes the support for the scores.

Description

Usage

Arguments

Value

References

Examples