QuaternaryProd (version 1.0.2)

QP_SigPvalue: Computes the p-value for a statistically significant score.

Description

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

Usage

QP_SigPvalue(score, q_p, q_m, q_z, q_r, n_p, n_m, n_z, epsilon = 1e-16, sig_level = 0.05)

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.

sig_level

Significance level of test hypothesis. Default value is 0.05.

Value

This function returns a numerical value, where the numerical value is the p-value of a score if the score is statistically significant otherwise it returns -1.

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. If the score is not statistically significant, then a value of -1 will be returned.

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

Examples

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