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| assessSymmetry | A function that calcualtes some directed degree statistics on graphs using a binomial error model |
| bpMatrix | This function generates the Bait-Prey Matrix for an protein-protein interaction (ppi) experiment |
| calcInOutDegStats | This function calculates the various degree statistic for a Protein-Protein Interaction (PPI) Graph |
| createSummaryTables | A function to create summary statistic tables for directed graphs |
| degreeEstimates | Estimate per-node degree in viable bait-prey (VBP) graph using maximum likelihood. |
| degreePMF | Estimate per-node degree in viable bait-prey (VBP) graph using maximum likelihood. |
| estErrProbMethodOfMoments | Estimate false positive and false negative error probabilities by method moments. |
| estimateCCMErrorRates | Estimate false positive and false negative error probabilities |
| estimatePPIErrorRates | Estimate false positive and false negative error probabilities for direct protein interactions |
| findAdjacent | A function that returns the set of prey detected by a bait in a bait-prey experiment. |
| findDegree | Estimate per-node degree in viable bait-prey (VBP) graph using maximum likelihood. |
| genBPGraph | A function to generate the protein-protein interaction (ppi) induced (un)directed graph |
| idHomodimers | A function to determine viable baits, viable preys, or homodimers within experimental data-sets. |
| idStochastic | A function to identify those proteins affected by either stochastic or systematic errors |
| idSystematic | A function to identify those proteins affected by either stochastic or systematic errors |
| idViableProteins | A function to determine viable baits, viable preys, or homodimers within experimental data-sets. |
| inOutScatterCharts | A function to create scatter plots of the in-degree and out-degree for each vertex of a directed graph |
| makeBinVect | A function to compute a permutation test on a two way table.h |
| nullDistDoublyTestedEdges | Null distribution of number of reciprocated, unreciprocated and missing edges in stochastic model. |
| ppiBuildParams4GO | A wrapper function to build a parameter class for the input of the HyperGTest. |
| ppiBuildParams4PFAM | A wrapper function to build a parameter class for the input of the HyperGTest. |
| ppiHGTest4GO | A wrapper function to implement the Hypergeometric test, HyperGTest found withing the Category and GOstats packages. |
| ppiHGTest4PFAM | A wrapper function to implement the Hypergeometric test, HyperGTest found withing the Category and GOstats packages. |
| separateExptBySize | A function to partition experiments in user defined small, medium, large scale experiments |
| twowayPERM | A function to compute a permutation test on a two way table.h |
| twPERM | A function to compute a permutation test on a two way table.h |
| viabilityCharts | A function to create summary bar charts for directed graphs |