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 |
list2Matrix |
A function to that maps a list representation of a hypergraph (equivalently a bipartite graph) graph to its corresponding sparse-matrix representation. |
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 |
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 |
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" |