# Protein-Protein Interaction Statistical Package

## Documentation for package ‘ppiStats’ version 1.16.0

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.

## Help Pages

assessSymmetry | A function that calcualtes some directed degree statistics on graphs
bpMatrix | This function generates the Bait-Prey Matrix for an protein-protein
calcInOutDegStats | This function calculates the various degree statistic for a
createSummaryTables | A function to create summary statistic tables for directed graphs
degreeEstimates | Estimate per-node degree in viable bait-prey (VBP) graph using maximum
degreePMF | Estimate per-node degree in viable bait-prey (VBP) graph using maximum
estErrProbMethodOfMoments | Estimate false positive and false negative error probabilities by
estimateCCMErrorRates | Estimate false positive and false negative error probabilities
estimatePPIErrorRates | Estimate false positive and false negative error probabilities for
findAdjacent | A function that returns the set of prey detected by a bait in a
findDegree | Estimate per-node degree in viable bait-prey (VBP) graph using maximum
genBPGraph | A function to generate the protein-protein interaction (ppi) induced
idHomodimers | A function to determine viable baits, viable preys, or homodimers
idStochastic | A function to identify those proteins affected by either stochastic or
idSystematic | A function to identify those proteins affected by either stochastic or
idViableProteins | A function to determine viable baits, viable preys, or homodimers
inOutScatterCharts | A function to create scatter plots of the in-degree and out-degree for
makeBinVect | A function to compute a permutation test on a two way table.h
nullDistDoublyTestedEdges | Null distribution of number of reciprocated, unreciprocated and missing
ppiBuildParams4GO | A wrapper function to build a parameter class for the input of the
ppiBuildParams4PFAM | A wrapper function to build a parameter class for the input of the
ppiHGTest4GO | A wrapper function to implement the Hypergeometric test, HyperGTest
ppiHGTest4PFAM | A wrapper function to implement the Hypergeometric test, HyperGTest
separateExptBySize | A function to partition experiments in user defined small, medium,
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