Desc                    A method to return a description of a protein
                        complex
ID                      A method to return the ID of a protein complex
JaccardCoef             A function to calculate the Jaccard similarity
                        index between two sets
ScISI                   The In Silico Interactome for Saccharomyces
                        cerevisiae
ScISI2html              A function that generates an html page for the
                        GO and MIPs protein complexes
arp23                   Constituent members of Protein Complex Arp 2/3
arp23G                  The graph of arg 2/3
arp23Orf                Constituent members of Protein Complex Arp 2/3
arp23Y2HG               A graph of ARP 2/3 containing only Y2H verified
                        interactions
calcGraphStats          A function to calculate the various summary
                        statistics for Y2H induced graphs
cfia                    Constituent members of Protein Complex Cleavage
                        Factor IA (CFIA)
cfiaOrf                 Constituent members of Protein Complex Cleavage
                        Factor IA (CFIA)
checkComplex            Function to check a list of protein complexes
                        wrt ScISI
checkSGN                A function to check that the protein names are
                        all systematic gene names.
compBijection           A recursive function that greedily handles the
                        alignment issue
compareComplex          A function to compare two bipartite graph
                        matrices
createGODataFrame       A function to create a Dataframe from the GO
                        protein complexes
createGOMatrix          A function to create the bipartite graph (BG)
                        incidence matrix from the protein complexes
                        parsed from the GO Database
createMipsDataFrame     A function that creates a data frame from the
                        MIPS Data
createMipsMatrix        A function to create the bipartite graph
                        incidence matrix from MIPS protein complexes
createYeastDataObj      Creates an object of class yeastData
dataS                   A character matrix containing the source data
                        for the ScISI
eAt                     An edge attribute data file
eAt2                    A file containing edge attributes
edgeProp                A function to estimate the edge proportion of a
                        y2h induced graph on a protein complex
egEBI16112              A graph example mapping an IntAct ID to
                        Systematic Gene Names
expStats                A data file containing the experimental
                        statistics
findSubComp             A function that looks for either equality
                        between two complexes or complete containment
                        of one complex in another
gavin2mergeMG           A data file containing the pre-merged Gavin to
                        (merged) MIPS-GO data
getAPMSData             A function to get the estimated complexes from
                        high throughput data determined by the package
                        apComplex.
getGOInfo               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.
getLocOrfs              A function to obtain ORFs for the ScISI
getMipsInfo             A function that reads the downloaded text file
                        from the MIPS repository and generates a named
                        list of protein complexes.
getURL                  A method to return an url location of a protein
                        complex
graphSumStats           An initiation function to generate graph
                        statistics
ho2mergeMGG             A data file containing the pre-merged Ho to the
                        (merged) MIPS-GO-Gavin data
krogan2mergeMGGH        A data file containing the pre-merged Krogan to
                        the (merged) MIPS-GO-Gavin-Ho data
locScISI                A data file used to estimate the location of
                        the complexes of the ScISI
mapping2SysG            A example graph of the mapping from IntAct to
                        Systematic Names
mappingsG               A example graph of the mapping from IntAct to
                        Systematic Names
maximizeSimilarity      A function compares two bipartite graph
                        matrices and finds the most similar matches
                        between the clusters
meanDeg                 A function to estimate the population mean
                        nodal degree of a protein complex of interest
mergeBGMat              A function that merges two bipartite graph (BG)
                        incidence matrices into one.
mips2go                 A data file containing the pre-merged GO to the
                        MIPS data
nAt                     A file containing node attributes
nAtMap                  A file containing node attributes
nonGenes                Genes found in MIPS which are not gene locus
                        names
nucComp                 A data file containing the nuclear complexes
recCompSize             A function that records the relative sizes of
                        complex C-i from one bipartite graph with
                        complex K-j from a different bipartite graph.
redundantM              A matrix of redundant complex summary
                        statistics
rmByEvi                 A function that parses through each GO protein
                        complex and removes proteins based on evidence
                        codes.
runAlignment            A function to establish preliminaries for the
                        compBijection function.
runCompareComplex       A function that calls all other types of
                        comparison functions
subCompM                A matrix of sub-complex summary statistics
sumStats                A function to calculate some summary statistics
                        between an two interactomes
unWantedComp            A function to manually remove protein complexes
                        from some in silico interactome
unwanted                GO terms that are parsed but not protein
                        complexes
xtraGO                  A character vector of hand selected GO protein
                        complexes
xtraGONodes             A function to check manually curated GO nodes
yeastData-class         Class "yeastData"
