x<-"hello"
require(IdMappingAnalysis)
options(stringsAsFactors = FALSE)
#### suggested to call: options(stringsAsFactors = FALSE)
################RUN ONLY ONCE UNTIL CORRECTED
Formatted_primary_data<-add_row_names_col(RPPADATA)
Formatted_secondary_data<-add_row_names_col(RNASEQDATA,exp_colname = "RNAseqWorkflow")
#################################
primaryIDs <- IdMapBase$primaryIDs(Formatted_primary_data);
secondaryIDs <- IdMapBase$primaryIDs(Formatted_secondary_data);
###########FIX THE ORDER OF ARGS ITS IS ANNOYING
idmap_rnaseqworkflow_df<-MakeWorkflowMap(Formatted_secondary_data,Formatted_primary_data)
#uniquePairs.rnaseq<-UniquePairs(idmap_rnaseqworkflow_df,primaryKey="Symbol",secondaryKey="RNAseqWorkflow")
IdMap_rna_rppa<-IdMap(DF=idmap_rnaseqworkflow_df,name="IdMap_rna_rppa", primaryKey="Symbol",secondaryKey="RNAseqWorkflow")
######################### unique pairs from the jointIdMap
#uniquePairsOvarian <- as.UniquePairs.IdMap(IdMap_NA_RPPA,secondaryIDsOvarian)
uniquePairs_workflow <- as.UniquePairs.IdMap(IdMap_rna_rppa,secondaryIDs)
corrData.rnaseq <- CorrData(uniquePairs_workflow,Formatted_primary_data,Formatted_secondary_data)
corr.rnarppa.try1 <- Corr(corrData.rnaseq,method="spearman",verbose=TRUE)
bootstrap.rnarppa<-Bootstrap(corrData.rnaseq,Fisher=TRUE,verbose=TRUE)
bootModel.rna.rppa <-as.data.frame(bootstrap.rnarppa)
bootModel.rna.rppa<-bootModel.rna.rppa[c(1:96,99:134),]
postProbs.rnarppa<- NULL
postProbVar.rnarppa<- NULL
EMtest.rnarppa<- fit2clusters.RNAseq(bootModel.rna.rppa$corr, bootModel.rna.rppa$sd^2,psi0Constraint=0, sameV=T,estimatesOnly=F,seed=Random.seed.save)
postProbsOvarian<-as.vector(EMtestOvarian[[1]]/(1+EMtestOvarian[[1]])) #not needed at the output is a datafrmae from fit2clusters
postProbVarOvarian <-as.vector(EMtestOvarian[[2]])
pairs <- jointUniquePairs$as.data.frame()
##########################
pairMatchTable<-pairs
#bootModel.fulldata<-as.data.frame(bootstrap)
bootModel <-as.data.frame(bootstrap)
load("dotRandom.seed.rda")
Random.seed.save <- sync.Random.seed <- .Random.seed
bootMergedWithPairs = merge(data.frame(postProbs=postProbs, postProbVar=postProbVar,bootModel), pairMatchTable)
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