Protein-Protein Interaction Statistical Package

---

Documentation for package ‘ppiStats’ version 1.59.4

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

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