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

View source: R/UserFunctions.R

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

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

`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. |

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.

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.

Carl Tony Fakhry, Ping Chen and Kourosh Zarringhalam

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'.

1 2 3 | ```
# Computing The p-value of score 50
# for the given table margins.
pval <- QP_SigPvalue(50,50,50,50,0,50,50,50)
``` |

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

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