In Silico Interactome


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Documentation for package ‘ScISI’ version 1.50.0

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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-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-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-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"