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 |