QuaternaryProd (version 1.0.2)

QP_Pmf: Computes the probability mass function of the scores.

Description

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.

Usage

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

Arguments

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.

Value

Vector of probabilities for scores in the support.

Details

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.

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'.

See Also

QP_Pvalue, QP_Support

Examples

# 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)