RDocumentation
Moon
Learn R
Search all packages and functions
ppiStats (version 1.38.0)
Protein-Protein Interaction Statistical Package
Description
Tools for the analysis of protein interaction data.
Copy Link
Copy
Link to current version
Version
Version
1.38.0
1.36.0
1.34.0
1.32.0
Down Chevron
Version
1.38.0
License
Artistic-2.0
Maintainer
Bioconductor Package Maintainer
Last Published
January 1st, 1970
Functions in ppiStats (1.38.0)
Search functions
calcInOutDegStats
This function calculates the various degree statistic for a Protein-Protein Interaction (PPI) Graph
viabilityCharts
A function to create summary bar charts for directed graphs
idProteinErrorType
A function to identify those proteins affected by either stochastic or systematic errors
findAdjacent
A function that returns the set of prey detected by a bait in a bait-prey experiment.
estimateCCMErrorRates
Estimate false positive and false negative error probabilities
idProteinType
A function to determine viable baits, viable preys, or homodimers within experimental data-sets.
degreeEstimates
Estimate per-node degree in viable bait-prey (VBP) graph using maximum likelihood.
createSummaryTables
A function to create summary statistic tables for directed graphs
assessSymmetry
A function that calcualtes some directed degree statistics on graphs using a binomial error model
genBPGraph
A function to generate the protein-protein interaction (ppi) induced (un)directed graph
inOutScatterCharts
A function to create scatter plots of the in-degree and out-degree for each vertex of a directed graph
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.
twPERM
A function to compute a permutation test on a two way table.h
estimatePPIErrorRates
Estimate false positive and false negative error probabilities for direct protein interactions
separateExptBySize
A function to partition experiments in user defined small, medium, large scale experiments
bpMatrix
This function generates the Bait-Prey Matrix for an protein-protein interaction (ppi) experiment
estErrProbMethodOfMoments
Estimate false positive and false negative error probabilities by method moments.
nullDistDoublyTestedEdges
Null distribution of number of reciprocated, unreciprocated and missing edges in stochastic model.