R/calcScores.R

In VCCRI/PGSCatalogCalculator: Downloads Scores From PGS Catalog

getFile <- function(inProfile){
  inFile <- getPGSProfileInFile(inProfile)
  inRecord <- getPGSProfileInRecord(inProfile)
  midSamples <- getPGSProfileMidSamples(inProfile)
  if(length(inFile) != 0 & file.exists(inFile)){
    inData <- data.table::fread(inFile, stringsAsFactors=FALSE)
    inData[,PGS_RECORD_ID := inRecord]
    inData <- inData[!(IID %in% midSamples),]
    #inData[,subject_type := "diseased"]
    return(data.table(inData))
  } else {
    return(NULL)
  }
}

getAggDf <- function(inProfiles){
  totalSamples <- data.table::rbindlist(lapply(inProfiles, getFile))
  aggSamples <- totalSamples[,sum(as.numeric(SCORESUM)), by=.(IID, PGS_RECORD_ID)]

  setnames(aggSamples, "V1", "PRS")
  return(aggSamples)
}