test1.R
In ScISI: In Silico Interactome

 library("ScISI")
##create the GO bipartite graph 
 go = getGOInfo(eCode=NULL, wantAllComplexes = FALSE)
 goCoded = getGOInfo(eCode=c("ISI","ND", "IPI"), toGrep = NULL, wantAllComplexes = FALSE)
 grepL = vector("list", length=1)
 grepL[[1]]$pattern = "\\Bsomal\\b"
 goPhrase = getGOInfo(eCode=NULL, toGrep = grepL, parseType = "grep", wantAllComplexes = TRUE)

##create the Bipartite graph matrix
 goM = createGOMatrix(go)

##create the data frame with all the corresponding information
 goDF = createGODataFrame(go, goM)

##create an instance of yeastData from the GO dataframe
 goOb = createYeastDataObj(goDF)

##create the mips bipartite graph
 mips = getMipsInfo(wantAllComplexes = FALSE)

##create the mips bipartite graph matrix
 mipsM = createMipsMatrix(mips)

##create the mips dataframe
 mipsDF = createMipsDataFrame(mips$DESC, mipsM)

##create an instance of the yeastData object from Mips dataframe
 mipsOb = createYeastDataObj(mipsDF)

##compare the complexes via Jaccard Index
cc = runCompareComplex(mipsM, goM, index="Jaccard", byWhich = "ROW")

##Some of the data stored in cc
cc$equal  ##those complexes that are equal
cc$subcomplex  ##those complexes that are subordinate to another
cc$maxIntersect ## since I set byWhich = "ROW" it will find the column complexes
                ## most similar to each row complex
cc$JC  ##The matrix of Jaccard Coefficients between the two bipartite graphs


##merging and removing the equal complexes
v2=mergeBGMat(mipsM,goM, cc$toBeRm)

##some of these are of length 1
s1= colSums(v2)

v3 = v2[,s1>1]

g1 = getAPMSData("Gavin")

#test to see if rm by code works:

nam = names(go)
sapply(nam, function(w) {setdiff(go[[w]], goCoded[[w]])})

###y2h stuff
mipsY2H = getMipsY2HInfo(wantDefault = TRUE, toGrep = NULL, parseType = NULL, eCode = NULL)

mipsPPI = createMipsY2HMatrix(mipsY2H)

###the arguments don't mean anything right now. there is a potential for something meaningful
###right now, the data from MIPS implies interaction can be ascertained from not only y2h but
###also co-immunoprecipitation, etc. i have grepped for those with "two hybrid" in the
###desc part of the file. this is prelim...Robert what else do you think we should default
###grep for? we can let others decide in the toGrep stuff.