ppiStats: Protein-Protein Interaction Statistical Package

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Tools for the analysis of protein interaction data.

Author
T. Chiang and D. Scholtens with contributions from W. Huber and L. Wang
Date of publication
None
Maintainer
Bioconductor Package Maintainer <maintainer@bioconductor.org>
License
Artistic-2.0
Version
1.40.0

View on Bioconductor

Man pages

assessSymmetry
A function that calcualtes some directed degree statistics on...
bpMatrix
This function generates the Bait-Prey Matrix for an...
calcInOutDegStats
This function calculates the various degree statistic for a...
createSummaryTables
A function to create summary statistic tables for directed...
degreeEstimates
Estimate per-node degree in viable bait-prey (VBP) graph...
estErrProbMethodOfMoments
Estimate false positive and false negative error...
estimateCCMErrorRates
Estimate false positive and false negative error...
estimatePPIErrorRates
Estimate false positive and false negative error...
findAdjacent
A function that returns the set of prey detected by a bait in...
genBPGraph
A function to generate the protein-protein interaction (ppi)...
hgParams
A wrapper function to build a parameter class for the input...
hgTests
A wrapper function to implement the Hypergeometric test,...
idProteinErrorType
A function to identify those proteins affected by either...
idProteinType
A function to determine viable baits, viable preys, or...
inOutScatterCharts
A function to create scatter plots of the in-degree and...
nullDistDoublyTestedEdges
Null distribution of number of reciprocated, unreciprocated...
separateExptBySize
A function to partition experiments in user defined small,...
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

Files in this package

ppiStats/DESCRIPTION
ppiStats/NAMESPACE
ppiStats/R
ppiStats/R/assessSymmetry.R
ppiStats/R/bpMatrix.R
ppiStats/R/calcInOutDegStats.R
ppiStats/R/degreeEstimates.R
ppiStats/R/estErrProbMethodOfMoments.R
ppiStats/R/estimateCCMErrorRates.R
ppiStats/R/estimatePPIErrorRates.R
ppiStats/R/findAdjacent.R
ppiStats/R/genBPGraph.R
ppiStats/R/idHomodimers.R
ppiStats/R/idStochastic.R
ppiStats/R/idSystematic.R
ppiStats/R/idViableProteins.R
ppiStats/R/nullDistDoublyTestedEdges.R
ppiStats/R/ppiHGTest.R
ppiStats/R/separateExptBySize.R
ppiStats/R/sumStatCharts.R
ppiStats/R/twPERM.R
ppiStats/build
ppiStats/build/vignette.rds
ppiStats/inst
ppiStats/inst/Scripts
ppiStats/inst/Scripts/hgGO.R
ppiStats/inst/Scripts/hgPfam.R
ppiStats/inst/doc
ppiStats/inst/doc/ppiStats.R
ppiStats/inst/doc/ppiStats.Rnw
ppiStats/inst/doc/ppiStats.pdf
ppiStats/inst/extdata
ppiStats/inst/extdata/PPI_18052006.tab
ppiStats/inst/extdata/PPIpos
ppiStats/inst/extdata/intacty2hppMatrix.rda
ppiStats/inst/extdata/supp.Rnw
ppiStats/inst/extdata/zzz.R
ppiStats/man
ppiStats/man/assessSymmetry.Rd
ppiStats/man/bpMatrix.Rd
ppiStats/man/calcInOutDegStats.Rd
ppiStats/man/createSummaryTables.Rd
ppiStats/man/degreeEstimates.Rd
ppiStats/man/estErrProbMethodOfMoments.Rd
ppiStats/man/estimateCCMErrorRates.Rd
ppiStats/man/estimatePPIErrorRates.Rd
ppiStats/man/findAdjacent.Rd
ppiStats/man/genBPGraph.Rd
ppiStats/man/hgParams.Rd
ppiStats/man/hgTests.Rd
ppiStats/man/idProteinErrorType.Rd
ppiStats/man/idProteinType.Rd
ppiStats/man/inOutScatterCharts.Rd
ppiStats/man/nullDistDoublyTestedEdges.Rd
ppiStats/man/separateExptBySize.Rd
ppiStats/man/twPERM.Rd
ppiStats/man/viabilityCharts.Rd
ppiStats/vignettes
ppiStats/vignettes/ppiStats.Rnw
ppiStats/vignettes/proteinReview.bib