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ppiStats (version 1.36.0)

Protein-Protein Interaction Statistical Package

Description

Tools for the analysis of protein interaction data.

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Version

Version

1.36.0

License

Artistic-2.0

Maintainer

Bioconductor Package Maintainer

Last Published

February 15th, 2017

Functions in ppiStats (1.36.0)

createSummaryTables

A function to create summary statistic tables for directed graphs
inOutScatterCharts

A function to create scatter plots of the in-degree and out-degree for each vertex of a directed graph
nullDistDoublyTestedEdges

Null distribution of number of reciprocated, unreciprocated and missing edges in stochastic model.
idProteinErrorType

A function to identify those proteins affected by either stochastic or systematic errors
idProteinType

A function to determine viable baits, viable preys, or homodimers within experimental data-sets.
genBPGraph

A function to generate the protein-protein interaction (ppi) induced (un)directed graph
assessSymmetry

A function that calcualtes some directed degree statistics on graphs using a binomial error model
findAdjacent

A function that returns the set of prey detected by a bait in a bait-prey experiment.
bpMatrix

This function generates the Bait-Prey Matrix for an protein-protein interaction (ppi) experiment
hgParams

A wrapper function to build a parameter class for the input of the HyperGTest.
hgTests

A wrapper function to implement the Hypergeometric test, HyperGTest found withing the Category and GOstats packages.
degreeEstimates

Estimate per-node degree in viable bait-prey (VBP) graph using maximum likelihood.
estimatePPIErrorRates

Estimate false positive and false negative error probabilities for direct protein interactions
viabilityCharts

A function to create summary bar charts for directed graphs
estimateCCMErrorRates

Estimate false positive and false negative error probabilities
twPERM

A function to compute a permutation test on a two way table.h
estErrProbMethodOfMoments

Estimate false positive and false negative error probabilities by method moments.
calcInOutDegStats

This function calculates the various degree statistic for a Protein-Protein Interaction (PPI) Graph
separateExptBySize

A function to partition experiments in user defined small, medium, large scale experiments