QP_Pvalue: Computes the p-value of a score.

Description

This function computes the right sided p-value for the Quaternary Dot Product Scoring Statistic.

Usage

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

Arguments

score

The score for which the p-value will be computed.

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

Threshold for probabilities of matrices. Default value is 1e-16.

Value

This function returns a numerical value, where the numerical value is the p-value of the score.

Details

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'.

Examples

Run this code

# Computing The p-value of score 50 
# for the given table margins. 
pval <- QP_Pvalue(50,50,50,50,0,50,50,50)

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