Estimate false positive and false negative error probabilities for complex comembership edges using a protein complex interactome gold standard

1 2 | ```
estimateCCMErrorRates(m,GS,filterSystematic=TRUE,
obsPropThresh=1,SystematicpThresh=.01)
``` |

`m` |
The bait to prey data adjacency matrix. Baits index the rows and prey index the columns. |

`GS` |
A gold standard protein complex interaction incidence matrix. Proteins index the rows and protein complexes index the columns. |

`filterSystematic` |
A logical. If TRUE, all baits with with highly uneven directed degree will be filtered out of the data. |

`obsPropThresh` |
A numeric between 0 and 1. The proportion of tested proteins found within a protein complex needed to keep that protein complex within the gold standard set. |

`SystematicpThresh` |
A numeric between 0 and 1. The p-value threshold by which systematic errors are filtered. |

The model is described in the manuscript
*Estimating node degree in bait-prey graphs.*
by D. Scholtens et al.

A list:

`globalpTP` |
A numeric between 0 and 1. Estimate of pTP. |

`globalpTPSE` |
A numeric. Estimate of standard error of globalpTP estimate. |

`globalpFP` |
A numeric between 0 and 1. Estimate of pFP. |

`pTP95CI` |
A vector of length 2. 95 percent confidence interval upper and lower bounds for globalpTP estimate. |

`pFP95CI` |
A vector of length 2. 95 percent confidence interval upper and lower bounds for globalpFP estimate. |

`nEligComplexes` |
A numeric. Number of complexes from GS that met obsPropThresh criteria. |

`nEligBaits` |
A numeric. Total number of eligible baits in GS set. |

`nEligEdges` |
A numeric. Total number of eligible edges in GS set. |

`nBaitsInComplexes` |
A vector. Number of baits in each eligible complex. |

`complexSizes` |
A vector. Size of each complex in GS set. |

T. Chiang and D. Scholtens

Scholtens D, Chiang T, Huber W, Gentleman R. Estimating node
degree in bait-prey graphs. *Bioinformatics*. To appear.

1 2 3 4 | ```
data(Ho2002BPGraph)
data(ScISIC)
Ho2002mat = as(Ho2002BPGraph,"matrix")
estimateCCMErrorRates(Ho2002mat,ScISIC)$globalpTP
``` |

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