# Protein-Protein Interaction Statistical Package

## Documentation for package ‘ppiStats’ version 1.8.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

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