Protein-Protein Interaction Statistical Package

Documentation for package ‘ppiStats’ version 1.16.0

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

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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