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

View source: R/UserFunctions.R

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

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

`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. |

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.

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

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'.

`QP_Pmf`

, `QP_Pvalue`

, `QP_SigPvalue`

1 2 3 | ```
# Computing The probability of score 50
# for the given table margins.
prob <- QP_Probability(0,50,50,50,0,50,50,50)
``` |

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