| 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... |
| cfia | Constituent members of Protein Complex Cleavage Factor IA... |
| cfiaOrf | Constituent members of Protein Complex Cleavage Factor IA... |
| checkComplex | Function to check a list of protein complexes wrt ScISI |
| checkSGN | A function to check that the protein names are all systematic... |
| compareComplex | A function to compare two bipartite graph matrices |
| compBijection | A recursive function that greedily handles the alignment... |
| createGODataFrame | A function to create a Dataframe from the GO protein... |
| createGOMatrix | A function to create the bipartite graph (BG) incidence... |
| createMipsDataFrame | A function that creates a data frame from the MIPS Data |
| createMipsMatrix | A function to create the bipartite graph incidence matrix... |
| createYeastDataObj | Creates an object of class yeastData |
| dataS | A character matrix containing the source data for the ScISI |
| Desc-methods | A method to return a description of a protein complex |
| eAt | An edge attribute data file |
| eAt2 | A file containing edge attributes |
| edgeProp | A function to estimate the edge proportion of a y2h induced... |
| 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... |
| gavin2mergeMG | A data file containing the pre-merged Gavin to (merged)... |
| getAPMSData | A function to get the estimated complexes from high... |
| getGOInfo | A function that parses through the GO database; it agreps for... |
| getLocOrfs | A function to obtain ORFs for the ScISI |
| getMipsInfo | A function that reads the downloaded text file from the MIPS... |
| getURL-methods | 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)... |
| ID-methods | A method to return the ID of a protein complex |
| JaccardCoef | A function to calculate the Jaccard similarity index between... |
| 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... |
| mapping2SysG | A example graph of the mapping from IntAct to Systematic... |
| mappingsG | A example graph of the mapping from IntAct to Systematic... |
| maximizeSimilarity | A function compares two bipartite graph matrices and finds... |
| meanDeg | A function to estimate the population mean nodal degree of a... |
| mergeBGMat | A function that merges two bipartite graph (BG) incidence... |
| 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... |
| redundantM | A matrix of redundant complex summary statistics |
| rmByEvi | A function that parses through each GO protein complex and... |
| runAlignment | A function to establish preliminaries for the compBijection... |
| runCompareComplex | A function that calls all other types of comparison functions |
| ScISI | The In Silico Interactome for Saccharomyces cerevisiae |
| ScISI2html | A function that generates an html page for the GO and MIPs... |
| subCompM | A matrix of sub-complex summary statistics |
| sumStats | A function to calculate some summary statistics between an... |
| unwanted | GO terms that are parsed but not protein complexes |
| unWantedComp | A function to manually remove protein complexes from some in... |
| xtraGO | A character vector of hand selected GO protein complexes |
| xtraGONodes | A function to check manually curated GO nodes |
| yeastData-class | Class "yeastData" |
