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 |