Entry: Desc
Aliases: Desc Desc,yeastData,character-method
Keywords: classes
Description: A method to return a description of a protein complex
URL: ../../../library/ScISI/html/Desc-methods.html

Entry: ID
Aliases: ID ID,yeastData,character-method
Keywords: classes
Description: A method to return the ID of a protein complex
URL: ../../../library/ScISI/html/ID-methods.html

Entry: JaccardCoef
Aliases: JaccardCoef
Keywords: datagen
Description: A function to calculate the Jaccard similarity index between two sets
URL: ../../../library/ScISI/html/JaccardCoef.html

Entry: ScISI
Aliases: ScISI
Keywords: datasets
Description: The In Silico Interactome for Saccharomyces cerevisiae
URL: ../../../library/ScISI/html/ScISI.html

Entry: ScISI2html
Aliases: ScISI2html
Keywords: datagen
Description: A function that generates an html page for the GO and MIPs protein complexes
URL: ../../../library/ScISI/html/ScISI2html.html

Entry: ScISIverified
Aliases: ScISIverified
Keywords: datasets
Description: The In Silico Interactome for Saccharomyces cerevisiae
URL: ../../../library/ScISI/html/ScISIverified.html

Entry: arp23
Aliases: arp23
Keywords: datasets
Description: Constituent members of Protein Complex Arp 2/3
URL: ../../../library/ScISI/html/arp23.html

Entry: arp23G
Aliases: arp23G
Keywords: datasets
Description: The graph of arg 2/3
URL: ../../../library/ScISI/html/arp23G.html

Entry: arp23Orf
Aliases: arp23Orf
Keywords: datasets
Description: Constituent members of Protein Complex Arp 2/3
URL: ../../../library/ScISI/html/arp23Orf.html

Entry: arp23Y2HG
Aliases: arp23Y2HG
Keywords: datasets
Description: A graph of ARP 2/3 containing only Y2H verified interactions
URL: ../../../library/ScISI/html/arp23Y2HG.html

Entry: calcGraphStats
Aliases: calcGraphStats
Keywords: datagen
Description: A function to calculate the various summary statistics for Y2H induced graphs
URL: ../../../library/ScISI/html/calcGraphStats.html

Entry: cfia
Aliases: cfia
Keywords: datasets
Description: Constituent members of Protein Complex Cleavage Factor IA (CFIA)
URL: ../../../library/ScISI/html/cfia.html

Entry: cfiaOrf
Aliases: cfiaOrf
Keywords: datasets
Description: Constituent members of Protein Complex Cleavage Factor IA (CFIA)
URL: ../../../library/ScISI/html/cfiaOrf.html

Entry: checkComplex
Aliases: checkComplex
Keywords: datagen
Description: Function to check a list of protein complexes wrt ScISI
URL: ../../../library/ScISI/html/checkComplex.html

Entry: checkSGN
Aliases: checkSGN
Keywords: datagen
Description: A function to check that the protein names are all systematic gene names.
URL: ../../../library/ScISI/html/checkSGN.html

Entry: compBijection
Aliases: compBijection
Keywords: array datagen
Description: A recursive function that greedily handles the alignment issue
URL: ../../../library/ScISI/html/compBijection.html

Entry: compareComplex
Aliases: compareComplex
Keywords: array datagen
Description: A function to compare two bipartite graph matrices
URL: ../../../library/ScISI/html/compareComplex.html

Entry: createGODataFrame
Aliases: createGODataFrame
Keywords: datagen
Description: A function to create a Dataframe from the GO protein complexes
URL: ../../../library/ScISI/html/createGODataFrame.html

Entry: createGOMatrix
Aliases: createGOMatrix
Keywords: datagen array
Description: A function to create the bipartite graph (BG) incidence matrix from the protein complexes parsed from the GO Database
URL: ../../../library/ScISI/html/createGOMatrix.html

Entry: createMipsDataFrame
Aliases: createMipsDataFrame
Keywords: datagen
Description: A function that creates a data frame from the MIPS Data
URL: ../../../library/ScISI/html/createMipsDataFrame.html

Entry: createMipsMatrix
Aliases: createMipsMatrix
Keywords: datagen array
Description: A function to create the bipartite graph incidence matrix from MIPS protein complexes
URL: ../../../library/ScISI/html/createMipsMatrix.html

Entry: createYeastDataObj
Aliases: createYeastDataObj
Keywords: classes
Description: Creates an object of class yeastData
URL: ../../../library/ScISI/html/createYeastDataObj.html

Entry: dataS
Aliases: dataS
Keywords: datasets
Description: A character matrix containing the source data for the ScISI
URL: ../../../library/ScISI/html/dataS.html

Entry: eAt
Aliases: eAt
Keywords: datasets
Description: An edge attribute data file
URL: ../../../library/ScISI/html/eAt.html

Entry: eAt2
Aliases: eAt2
Keywords: datasets
Description: A file containing edge attributes
URL: ../../../library/ScISI/html/eAt2.html

Entry: edgeProp
Aliases: edgeProp
Keywords: datagen
Description: A function to estimate the edge proportion of a y2h induced graph on a protein complex
URL: ../../../library/ScISI/html/edgeProp.html

Entry: egEBI16112
Aliases: egEBI16112
Keywords: datasets
Description: A graph example mapping an IntAct ID to Systematic Gene Names
URL: ../../../library/ScISI/html/egEBI16112.html

Entry: expStats
Aliases: expStats
Keywords: datasets
Description: A data file containing the experimental statistics
URL: ../../../library/ScISI/html/expStats.html

Entry: findSubComp
Aliases: findSubComp
Keywords: datagen array
Description: A function that looks for either equality between two complexes or complete containment of one complex in another
URL: ../../../library/ScISI/html/findSubComp.html

Entry: gavin2mergeMG
Aliases: gavin2mergeMG
Keywords: datasets
Description: A data file containing the pre-merged Gavin to (merged) MIPS-GO data
URL: ../../../library/ScISI/html/gavin2mergeMG.html

Entry: getAPMSData
Aliases: getAPMSData
Keywords: datagen array
Description: A function to get the estimated complexes from high throughput data determined by the package apComplex.
URL: ../../../library/ScISI/html/getAPMSData.html

Entry: getGOInfo
Aliases: getGOInfo
Keywords: datagen
Description: A function that parses through the GO database; it agreps for the term "complex" and greps suffixes "-ase" and "-some" and returns nodes whose description contains such terms.
URL: ../../../library/ScISI/html/getGOInfo.html

Entry: getLocOrfs
Aliases: getLocOrfs
Keywords: datagen
Description: A function to obtain ORFs for the ScISI
URL: ../../../library/ScISI/html/getLocOrfs.html

Entry: getMipsInfo
Aliases: getMipsInfo
Keywords: datagen
Description: A function that reads the downloaded text file from the MIPS repository and generates a named list of protein complexes.
URL: ../../../library/ScISI/html/getMipsInfo.html

Entry: getURL
Aliases: getURL getURL,yeastData,character-method
Keywords: classes
Description: A method to return an url location of a protein complex
URL: ../../../library/ScISI/html/getURL-methods.html

Entry: graphSumStats
Aliases: graphSumStats
Keywords: datagen
Description: An initiation function to generate graph statistics
URL: ../../../library/ScISI/html/graphSumStats.html

Entry: ho2mergeMGG
Aliases: ho2mergeMGG
Keywords: datasets
Description: A data file containing the pre-merged Ho to the (merged) MIPS-GO-Gavin data
URL: ../../../library/ScISI/html/ho2mergeMGG.html

Entry: krogan2mergeMGGH
Aliases: krogan2mergeMGGH
Keywords: datasets
Description: A data file containing the pre-merged Krogan to the (merged) MIPS-GO-Gavin-Ho data
URL: ../../../library/ScISI/html/krogan2mergeMGGH.html

Entry: locScISI
Aliases: locScISI
Keywords: datasets
Description: A data file used to estimate the location of the complexes of the ScISI
URL: ../../../library/ScISI/html/locScISI.html

Entry: mapping2SysG
Aliases: mapping2SysG
Keywords: datasets
Description: A example graph of the mapping from IntAct to Systematic Names
URL: ../../../library/ScISI/html/mapping2SysG.html

Entry: mappingsG
Aliases: mappingsG
Keywords: datasets
Description: A example graph of the mapping from IntAct to Systematic Names
URL: ../../../library/ScISI/html/mappingG.html

Entry: maximizeSimilarity
Aliases: maximizeSimilarity
Keywords: datagen
Description: A function compares two bipartite graph matrices and finds the most similar matches between the clusters
URL: ../../../library/ScISI/html/maximizeSimilarity.html

Entry: meanDeg
Aliases: meanDeg
Keywords: datagen
Description: A function to estimate the population mean nodal degree of a protein complex of interest
URL: ../../../library/ScISI/html/meanDeg.html

Entry: mergeBGMat
Aliases: mergeBGMat
Keywords: datagen array
Description: A function that merges two bipartite graph (BG) incidence matrices into one.
URL: ../../../library/ScISI/html/mergeBGMat.html

Entry: mips2go
Aliases: mips2go
Keywords: datasets
Description: A data file containing the pre-merged GO to the MIPS data
URL: ../../../library/ScISI/html/mips2go.html

Entry: nAt
Aliases: nAt
Keywords: datasets
Description: A file containing node attributes
URL: ../../../library/ScISI/html/nAt.html

Entry: nAtMap
Aliases: nAtMap
Keywords: datasets
Description: A file containing node attributes
URL: ../../../library/ScISI/html/nAtMap.html

Entry: nucComp
Aliases: nucComp
Keywords: datasets
Description: A data file containing the nuclear complexes
URL: ../../../library/ScISI/html/nucComp.html

Entry: recCompSize
Aliases: recCompSize
Keywords: datagen
Description: A function that records the relative sizes of complex C-i from one bipartite graph with complex K-j from a different bipartite graph.
URL: ../../../library/ScISI/html/recCompSize.html

Entry: redundantM
Aliases: redundantM
Keywords: datasets
Description: A matrix of redundant complex summary statistics
URL: ../../../library/ScISI/html/redundantM.html

Entry: rmByEvi
Aliases: rmByEvi
Keywords: datagen
Description: A function that parses through each GO protein complex and removes proteins based on evidence codes.
URL: ../../../library/ScISI/html/rmByEvi.html

Entry: runAlignment
Aliases: runAlignment
Keywords: array datagen
Description: A function to establish preliminaries for the compBijection function.
URL: ../../../library/ScISI/html/runAlignment.html

Entry: runCompareComplex
Aliases: runCompareComplex
Keywords: datagen
Description: A function that calls all other types of comparison functions
URL: ../../../library/ScISI/html/runCompareComplex.html

Entry: subCompM
Aliases: subCompM
Keywords: datasets
Description: A matrix of sub-complex summary statistics
URL: ../../../library/ScISI/html/subCompM.html

Entry: sumStats
Aliases: sumStats
Keywords: datagen
Description: A function to calculate some summary statistics between an two interactomes
URL: ../../../library/ScISI/html/sumStats.html

Entry: unWantedComp
Aliases: unWantedComp
Keywords: datagen
Description: A function to manually remove protein complexes from some in silico interactome
URL: ../../../library/ScISI/html/unWantedComp.html

Entry: xtraGO
Aliases: xtraGO
Keywords: datasets
Description: A character vector of hand selected GO protein complexes
URL: ../../../library/ScISI/html/xtraGO.html

Entry: xtraGONodes
Aliases: xtraGONodes
Keywords: datagen
Description: A function to check manually curated GO nodes
URL: ../../../library/ScISI/html/xtraGONodes.html

Entry: yeastData-class
Aliases: yeastData-class yeastData
Keywords: classes
Description: Class "yeastData"
URL: ../../../library/ScISI/html/yeastData-class.html
