# In Silico Interactome

## Documentation for package ‘ScISI’ version 1.14.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

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.
compareComplex | A function to compare two bipartite graph matrices
compBijection | A recursive function that greedily handles the alignment issue
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
Desc | A method to return a description of a protein complex
Desc,yeastData,character-method | 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 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
getURL,yeastData,character-method | 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
ID | A method to return the ID of a protein complex
ID,yeastData,character-method | A method to return the ID of a protein complex
JaccardCoef | A function to calculate the Jaccard similarity index between two sets
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
ScISI | The In Silico Interactome for Saccharomyces cerevisiae
ScISI2html | A function that generates an html page for the GO and MIPs protein complexes
ScISIC | The In Silico Interactome for Saccharomyces cerevisiae
ScISIverified | The In Silico Interactome for Saccharomyces cerevisiae
subCompM | A matrix of sub-complex summary statistics
sumStats | A function to calculate some summary statistics between an two interactomes
unwanted | GO terms that are parsed but not protein complexes
unWantedComp | A function to manually remove protein complexes from some in silico interactome
xtraGO | A character vector of hand selected GO protein complexes
xtraGONodes | A function to check manually curated GO nodes
yeastData | Class "yeastData"
yeastData-class | Class "yeastData"