Entry: assessSymmetry
Aliases: assessSymmetry
Keywords: datagen
Description: A function that calcualtes some directed degree statistics on graphs using a binomial error model
URL: ../../../library/ppiStats/html/assessSymmetry.html

Entry: bpMatrix
Aliases: bpMatrix
Keywords: datagen
Description: This function generates the Bait-Prey Matrix for an protein-protein interaction (ppi) experiment
URL: ../../../library/ppiStats/html/bpMatrix.html

Entry: calcInOutDegStats
Aliases: calcInOutDegStats
Keywords: datagen
Description: This function calculates the various degree statistic for a Protein-Protein Interaction (PPI) Graph
URL: ../../../library/ppiStats/html/calcInOutDegStats.html

Entry: createSummaryTables
Aliases: createSummaryTables
Keywords: datagen
Description: A function to create summary statistic tables for directed graphs
URL: ../../../library/ppiStats/html/createSummaryTables.html

Entry: degreeEstimates
Aliases: degreeEstimates degreePMF findDegree
Keywords: graphs
Description: Estimate per-node degree in viable bait-prey (VBP) graph using maximum likelihood.
URL: ../../../library/ppiStats/html/degreeEstimates.html

Entry: estErrProbMethodOfMoments
Aliases: estErrProbMethodOfMoments
Keywords: manip
Description: Estimate false positive and false negative error probabilities by method moments.
URL: ../../../library/ppiStats/html/estErrProbMethodOfMoments.html

Entry: estimateCCMErrorRates
Aliases: estimateCCMErrorRates
Keywords: manip
Description: Estimate false positive and false negative error probabilities
URL: ../../../library/ppiStats/html/estimateCCMErrorRates.html

Entry: estimatePPIErrorRates
Aliases: estimatePPIErrorRates
Keywords: manip
Description: Estimate false positive and false negative error probabilities for direct protein interactions
URL: ../../../library/ppiStats/html/estimatePPIErrorRates.html

Entry: findAdjacent
Aliases: findAdjacent
Keywords: graphs
Description: A function that returns the set of prey detected by a bait in a bait-prey experiment.
URL: ../../../library/ppiStats/html/findAdjacent.html

Entry: genBPGraph
Aliases: genBPGraph
Keywords: datagen
Description: A function to generate the protein-protein interaction (ppi) induced (un)directed graph
URL: ../../../library/ppiStats/html/genBPGraph.html

Entry: hgParams
Aliases: ppiBuildParams4GO ppiBuildParams4PFAM
Keywords: datagen
Description: A wrapper function to build a parameter class for the input of the HyperGTest.
URL: ../../../library/ppiStats/html/hgParams.html

Entry: hgTests
Aliases: ppiHGTest4GO ppiHGTest4PFAM
Keywords: datagen
Description: A wrapper function to implement the Hypergeometric test, HyperGTest found withing the Category and GOstats packages.
URL: ../../../library/ppiStats/html/hgTests.html

Entry: idProteinErrorType
Aliases: idSystematic idStochastic
Keywords: datagen
Description: A function to identify those proteins affected by either stochastic or systematic errors
URL: ../../../library/ppiStats/html/idProteinErrorType.html

Entry: idProteinType
Aliases: idViableProteins idHomodimers
Keywords: datagen
Description: A function to determine viable baits, viable preys, or homodimers within experimental data-sets.
URL: ../../../library/ppiStats/html/idProteinType.html

Entry: inOutScatterCharts
Aliases: inOutScatterCharts
Keywords: datagen
Description: A function to create scatter plots of the in-degree and out-degree for each vertex of a directed graph
URL: ../../../library/ppiStats/html/inOutScatterCharts.html

Entry: nullDistDoublyTestedEdges
Aliases: nullDistDoublyTestedEdges
Keywords: manip
Description: Null distribution of number of reciprocated, unreciprocated and missing edges in stochastic model.
URL: ../../../library/ppiStats/html/nullDistDoublyTestedEdges.html

Entry: separateExptBySize
Aliases: separateExptBySize
Keywords: manip
Description: A function to partition experiments in user defined small, medium, large scale experiments
URL: ../../../library/ppiStats/html/separateExptBySize.html

Entry: twPERM
Aliases: twPERM twowayPERM makeBinVect
Keywords: datagen
Description: A function to compute a permutation test on a two way table.h
URL: ../../../library/ppiStats/html/twPERM.html

Entry: viabilityCharts
Aliases: viabilityCharts
Keywords: datagen
Description: A function to create summary bar charts for directed graphs
URL: ../../../library/ppiStats/html/viabilityCharts.html
