R/deployNetworkSparsity.R

In blogsdon/utilityFunctions:

# generateStatistics <- function(networkId,backgroundId){
#   networkObj <- synGet(networkId)
#   backgroundObj <- synGet(backgroundId)
#
#   loadNetwork <- function(file){
#     library(data.table)
#     sparrowNetwork <- data.table::fread(file,stringsAsFactors=FALSE,data.table=F)
#     rownames(sparrowNetwork) <- sparrowNetwork$V1
#     sparrowNetwork <- sparrowNetwork[,-1]
#     gc()
#     return(sparrowNetwork)
#   }
#
#   network <- loadNetwork(networkObj@filePath)
#   load(backgroundObj@filePath)
#   library(ROCR)
#
#   upperTriangular = which(upper.tri(network))
#   predvec <- as.matrix(network)[upperTriangular]
#   truevec <- as.matrix(net2)[upperTriangular]
#   predictionObj <- prediction(predvec,truevec)
#   return(predictionObj)
#
# }
#
# whichInteractionMatrix = function(file.tissueTypeAbrv,file.study){
#   if(file.tissueTypeAbrv=='DLPFC' & file.study=='CMC'){
#     return('syn5996138')
#   }else if(file.tissueTypeAbrv=='ACC' & file.study=='CMC'){
#     return('syn5996140')
#   }else if(file.tissueTypeAbrv=='DLPFC' & file.study=='HBCC'){
#     return('syn5996133')
#   }else if(file.tissueTypeAbrv=='DLPFC' & file.study=='ROSMAP'){
#     return('syn5996136')
#   }else{
#     return(NA)
#   }
# }
#
# require(synapseClient)
# synapseLogin()
#
#
# foo <- synQuery('select name,id,study,tissueTypeAbrv,disease,cogdx,fileType from file where projectId==\'syn5584871\' and analysisType==\'statisticalNetworkReconstruction\'')
#
# library(dplyr)
# foo2 <- filter(foo,!is.na(file.tissueTypeAbrv) & !is.na(file.study))
# interactionReference<- mapply(whichInteractionMatrix,foo2$file.tissueTypeAbrv,foo2$file.study,SIMPLIFY = TRUE)
# foo2 <- cbind(foo2,interactionReference)
#
# foo2 <- filter(foo2,file.fileType=='csv' & !is.na(interactionReference))
# View(foo2)
#
# foo2$resultLocation <- sapply(foo2$file.id,rSynapseUtilities::getGrandParent)
#
#
# statMech<-generateStatistics(backgroundId='syn5996140',networkId='syn5819902')