Protein-Protein Interaction Statistical Package


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Documentation for package ‘ppiStats’ version 1.4.1

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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
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.
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.
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.
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