QP_Pvalue: Computes the p-value of a score.

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

View source: R/UserFunctions.R

Description

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

Usage

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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.

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.

Value

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

Author(s)

Carl Tony Fakhry, Ping Chen and Kourosh Zarringhalam

References

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'.

See Also

QP_SigPvalue

Examples

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

QuaternaryProd documentation built on Nov. 8, 2020, 8:23 p.m.