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
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
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
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
createMipsDataFrame     A function that creates a data frame from the
                        MIPS Data
createMipsMatrix        A function to create the bipartite graph
                        incidence matrix from MIPS
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
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
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
getGOInfo               A function that parses through the GO database;
                        it agreps for the term
getLocOrfs              A function to obtain ORFs for the ScISI
getMipsInfo             A function that reads the downloaded text file
                        from the MIPS repository
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
krogan2mergeMGGH        A data file containing the pre-merged Krogan to
                        the (merged)
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
meanDeg                 A function to estimate the population mean
                        nodal degree of a protein
mergeBGMat              A function that merges two bipartite graph (BG)
                        incidence matrices into
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
redundantM              A matrix of redundant complex summary
                        statistics
rmByEvi                 A function that parses through each GO protein
                        complex and removes
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
unWantedComp            A function to manually remove protein complexes
                        from some in silico
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"
