QP_Probability {QuaternaryProd} | R Documentation

## Computes the probability of a score.

### Description

This function computes the probability of a score in the Quaternary Dot Product scoring distribution.

### Usage

    QP_Probability(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 probability 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.

For computing p-values, the user is advised to use the p-value function which is optimized for such purposes.

### Value

This function returns a numerical value, where the numerical value is the probability 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_Pmf`, `QP_Pvalue`, `QP_SigPvalue`

### Examples

    # Computing The probability of score 50
    # for the given table margins.
    prob <- QP_Probability(0,50,50,50,0,50,50,50)

[Package QuaternaryProd version 1.14.0 Index]