R/pullExpressionAndPhenoWinsorized.R

In Sage-Bionetworks/AMPAD:

pullExpressionAndPhenoWinsorized = function(){

  synapseClient::synapseLogin()
  library(dplyr)
  #get synIds for gene expression variables
  geneExpressionDataManifest <- synapseClient::synTableQuery("SELECT * FROM syn8681664 where dataType = 'mRNA' and columnScaled = 'TRUE'")

  #get synIds for covariates
  covariateManifest <- synapseClient::synTableQuery("SELECT * FROM syn9704300 WHERE ( ( normalizationType = 'CQN' ) AND ( dataSubType = 'covariates' ) )")

  #geneExpressionDataObj <- sapply(geneExpressionDataManifest@values$id,synapseClient::synGet)
  #covariateManifestObj <- sapply(covariateManifest@values$id,synapseClient::synGet)

  #load expression data into R
  geneExpressionList <- rSynapseUtilities::loadDelimIntoList(geneExpressionDataManifest@values$id)

  #load covariate data into R
  covariateList <- rSynapseUtilities::loadDelimIntoList(covariateManifest@values$id)
  covariateList$syn8484996 <- synapseClient::synGet('syn8484996',version = 8) %>%
    synapseClient::getFileLocation() %>%
    data.table::fread(data.table=F)

  covariateList$syn8456631 <- synapseClient::synGet('syn8456631',version = 15) %>%
    synapseClient::getFileLocation() %>%
    data.table::fread(data.table=F)

  covariateList$syn8466814 <- synapseClient::synGet('syn8466814',version = 12) %>%
    synapseClient::getFileLocation() %>%
    data.table::fread(data.table=F)

  #split mayo into two data-frames
  geneExpressionForAnalysis <- list()
  geneExpressionForAnalysis$mayoTCX <- geneExpressionList$syn8303274
  colnames(geneExpressionForAnalysis$mayoTCX)[1] <- 'aSampleId'


  geneExpressionForAnalysis$mayoCER <- geneExpressionList$syn8303281
  colnames(geneExpressionForAnalysis$mayoCER)[1] <- 'aSampleId'
  library(dplyr)
  #rosmap
  geneExpressionForAnalysis$rosmapDLPFC <- geneExpressionList$syn8303260
  colnames(geneExpressionForAnalysis$rosmapDLPFC)[1] <- 'aSampleId'
  #msbb
  geneExpressionForAnalysis$msbbFP <- geneExpressionList$syn8303298
  colnames(geneExpressionForAnalysis$msbbFP)[1] <- 'aSampleId'

  geneExpressionForAnalysis$msbbSTG <- geneExpressionList$syn8303308
  colnames(geneExpressionForAnalysis$msbbSTG)[1] <- 'aSampleId'

  geneExpressionForAnalysis$msbbPHG <- geneExpressionList$syn8303314
  colnames(geneExpressionForAnalysis$msbbPHG)[1] <- 'aSampleId'

  geneExpressionForAnalysis$msbbIFG <- geneExpressionList$syn8303338
  colnames(geneExpressionForAnalysis$msbbIFG)[1] <- 'aSampleId'


  ####transpose all matrices
  #geneExpressionForAnalysis <- lapply(geneExpressionForAnalysis,t)

  ####make data frames
  geneExpressionForAnalysis <- lapply(geneExpressionForAnalysis,data.frame,stringsAsFactors=FALSE)

  ####add sample id as first column
  #addSampleId <- function(x){
  #  x <- dplyr::mutate(x,aSampleId=rownames(x))
  #  return(x)
  #}
  #geneExpressionForAnalysis <- lapply(geneExpressionForAnalysis,addSampleId)


  #add diagnosis to each expression data frame with left join
  #mayo
  geneExpressionForAnalysis$mayoTCX <- dplyr::left_join(geneExpressionForAnalysis$mayoTCX,
                                                        covariateList$syn8466814%>%dplyr::select(SampleID,BrainRegion.Diagnosis),
                                                        c('aSampleId'='SampleID'))
  #w1<-which(colnames(geneExpressionForAnalysis$mayoTCX)%in%c('aSampleId','BrainRegion.Diagnosis'))
  #otherCol <- setdiff(1:ncol(geneExpressionForAnalysis$mayoTCX),w1)
  #geneExpressionForAnalysis$mayoTCX <- geneExpressionForAnalysis$mayoTCX[,c(w1,otherCol)]
  #colnames(geneExpressionForAnalysis$mayoTCX)[c(1,2)] <- c('SampleID','Diagnosis')

  logitDiag <- sapply(geneExpressionForAnalysis$mayoTCX$BrainRegion.Diagnosis,function(x){
    if(x=='TCX.AD'){
      return(1)
    }else if (x =='TCX.CONTROL'){
      return(0)
    }else{
      return(NA)
    }
  })
  mayoTCX <- dplyr::mutate(geneExpressionForAnalysis$mayoTCX,
                           logitDiagnosis = logitDiag)

  geneExpressionForAnalysis$mayoTCX <- mayoTCX




  geneExpressionForAnalysis$mayoCER <- dplyr::left_join(geneExpressionForAnalysis$mayoCER,
                                                        covariateList$syn8466814%>%dplyr::select(SampleID,BrainRegion.Diagnosis),
                                                        c('aSampleId'='SampleID'))
  #w1<-which(colnames(geneExpressionForAnalysis$mayoCER)%in%c('aSampleId','BrainRegion.Diagnosis'))
  #otherCol <- setdiff(1:ncol(geneExpressionForAnalysis$mayoCER),w1)
  #geneExpressionForAnalysis$mayoCER <- geneExpressionForAnalysis$mayoCER[,c(w1,otherCol)]
  #colnames(geneExpressionForAnalysis$mayoCER)[c(1,2)] <- c('SampleID','Diagnosis')

  logitDiag <- sapply(geneExpressionForAnalysis$mayoCER$BrainRegion.Diagnosis,function(x){
    if(x=='CER.AD'){
      return(1)
    }else if (x =='CER.CONTROL'){
      return(0)
    }else{
      return(NA)
    }
  })
  mayoCER <- dplyr::mutate(geneExpressionForAnalysis$mayoCER,
                           logitDiagnosis = logitDiag)
  geneExpressionForAnalysis$mayoCER <- mayoCER


  ###rosmap
  geneExpressionForAnalysis$rosmapDLPFC <- dplyr::left_join(geneExpressionForAnalysis$rosmapDLPFC,
                                                            covariateList$syn8456631%>%dplyr::select(SampleID,Diagnosis),
                                                            c('aSampleId'='SampleID'))
  #w1<-which(colnames(geneExpressionForAnalysis$rosmapDLPFC)%in%c('aSampleId','Diagnosis'))
  #otherCol <- setdiff(1:ncol(geneExpressionForAnalysis$rosmapDLPFC),w1)
  #geneExpressionForAnalysis$rosmapDLPFC <- geneExpressionForAnalysis$rosmapDLPFC[,c(w1,otherCol)]
  #colnames(geneExpressionForAnalysis$rosmapDLPFC)[c(1,2)] <- c('SampleID','Diagnosis')

  logitDiag <- sapply(geneExpressionForAnalysis$rosmapDLPFC$Diagnosis,function(x){
    if(x=='AD'){
      return(1)
    }else if (x =='CONTROL'){
      return(0)
    }else{
      return(NA)
    }
  })
  geneExpressionForAnalysis$rosmapDLPFC <- dplyr::mutate(geneExpressionForAnalysis$rosmapDLPFC,
                                                         logitDiagnosis = logitDiag)


  ####mssm

  geneExpressionForAnalysis$msbbFP <- dplyr::left_join(geneExpressionForAnalysis$msbbFP,
                                                       covariateList$syn8484996%>%dplyr::select(SampleID,BrainRegion.Diagnosis),
                                                       c('aSampleId'='SampleID'))


  geneExpressionForAnalysis$msbbSTG <- dplyr::left_join(geneExpressionForAnalysis$msbbSTG,
                                                        covariateList$syn8484996%>%dplyr::select(SampleID,BrainRegion.Diagnosis),
                                                        c('aSampleId'='SampleID'))


  geneExpressionForAnalysis$msbbPHG <- dplyr::left_join(geneExpressionForAnalysis$msbbPHG,
                                                        covariateList$syn8484996%>%dplyr::select(SampleID,BrainRegion.Diagnosis),
                                                        c('aSampleId'='SampleID'))


  geneExpressionForAnalysis$msbbIFG <- dplyr::left_join(geneExpressionForAnalysis$msbbIFG,
                                                        covariateList$syn8484996%>%dplyr::select(SampleID,BrainRegion.Diagnosis),
                                                        c('aSampleId'='SampleID'))


  logitDiag <- sapply(geneExpressionForAnalysis$msbbFP$BrainRegion.Diagnosis,function(x){
    if(x=='FP.AD'){
      return(1)
    }else if (x =='FP.CONTROL'){
      return(0)
    }else{
      return(NA)
    }
  })
  geneExpressionForAnalysis$msbbFP <- dplyr::mutate(geneExpressionForAnalysis$msbbFP,
                                                    logitDiagnosis = logitDiag)


  logitDiag <- sapply(geneExpressionForAnalysis$msbbSTG$BrainRegion.Diagnosis,function(x){
    if(x=='STG.AD'){
      return(1)
    }else if (x =='STG.CONTROL'){
      return(0)
    }else{
      return(NA)
    }
  })
  geneExpressionForAnalysis$msbbSTG <- dplyr::mutate(geneExpressionForAnalysis$msbbSTG,
                                                     logitDiagnosis = logitDiag)

  logitDiag <- sapply(geneExpressionForAnalysis$msbbPHG$BrainRegion.Diagnosis,function(x){
    if(x=='PHG.AD'){
      return(1)
    }else if (x =='PHG.CONTROL'){
      return(0)
    }else{
      return(NA)
    }
  })
  geneExpressionForAnalysis$msbbPHG <- dplyr::mutate(geneExpressionForAnalysis$msbbPHG,
                                                     logitDiagnosis = logitDiag)

  logitDiag <- sapply(geneExpressionForAnalysis$msbbIFG$BrainRegion.Diagnosis,function(x){
    if(x=='IFG.AD'){
      return(1)
    }else if (x =='IFG.CONTROL'){
      return(0)
    }else{
      return(NA)
    }
  })
  geneExpressionForAnalysis$msbbIFG <- dplyr::mutate(geneExpressionForAnalysis$msbbIFG,
                                                     logitDiagnosis = logitDiag)

  return(geneExpressionForAnalysis)
}