QP_Pmf: Computes the probability mass function of the scores.
In QuaternaryProd: Computes the Quaternary Dot Product Scoring Statistic for Signed and Unsigned Causal Graphs

Description Usage Arguments Details Value Author(s) References See Also Examples

This function computes the probability mass function for the Quaternary Dot Product Scoring Statistic for signed causal graphs. This includes scores with probabilities strictly greater than zero.

1	QP_Pmf(q_p, q_m, q_z, q_r, n_p, n_m, n_z, epsilon = 1e-16)

`q_p`	Expected number of positive predictions.
`q_m`	Expected number of negative predictions.
`q_z`	Expected number of nil predictions.
`q_r`	Expected number of regulated predictions.
`n_p`	Number of positive predictions from experiments.
`n_m`	Number of negative predictions from experiments.
`n_z`	Number of nil predictions from experiments.
`epsilon`	parameter for thresholding probabilities of matrices. Default value is 1e-16.

This function computes the probability for each score in the support of the distribution. The returned value is a vector of probabilities where the returned vector has names set equal to the corresponding scores.

Setting epsilon to zero will compute the probability mass function without ignoring any matrices with probabilities smaller than epsilon*D_max (D_max is the numerator associated with the matrix of highest probability for the given constraints). The default value of 1e-16 is experimentally validated to be a very reasonable threshold. Setting the threshold to higher values which are smaller than 1 will lead to understimating the probabilities of each score since more tables will be ignored.

Vector of probabilities for scores in the support.

Carl Tony Fakhry, Ping Chen and Kourosh Zarringhalam

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'.

QP_Pvalue, QP_Support

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# Compute the probability mass function of the Quaternary Dot
# Product Scoring Statistic for the given table margins.
pmf <- QP_Pmf(50,50,50,0,50,50,50)