R/mts_GeneDepID.R

In MultiSEp: Predict Synthetic Lethality and Other Gene Dependency Relationships from Multiomics Data

mts_GeneDepID = function(exprsMatrix = exprsMatrix, crisprMatrix = crisprMatrix, cores = cores, fcVal=fcVal, pVal=pVal, tissueMatrix=tissueMatrix) {
  # Error catching - from input
  if(missing(cores))
  {
    cores <- 1
    message("1 core selected")
  } else if(cores == 0)
  {
    stop("cores should be >= 1")
  } else {
    message(paste(cores, " cores selected", sep=""))
  }
  
  if(missing(fcVal))
  {
    fcVal <- 0.1
    message("Fold Change Threshold not entered, using 0.1")
  } else {
    message(paste("Fold Change Threshold: ", fcVal, sep=""))
  }
  
  if(missing(pVal))
  {
    pVal <- 0.1
    message("P-Value Threshold not entered, using 0.1")
  } else {
    message(paste("P Value Threshold: ", pVal, sep=""))
  }
  
  if(missing(exprsMatrix))
  {
    stop("No Expression Matrix Provided")
  } else {
    if (!is.data.frame(exprsMatrix)) {
      stop("exprsMatrix must be a data frame")
      return(NULL)
    }
  }
  
  if(missing(crisprMatrix))
  {
    stop("No CRISPR Matrix Provided")
  } else {
    if (!is.data.frame(crisprMatrix)) {
      stop("crisprMatrix must be a data frame")
      return(NULL)
    }
  } 
  
  if(missing(tissueMatrix))
  {
    message("No Tissue Matrix Provided: Function will not perform the tissue-specific step")
    message("Running mts_clusterAvg")
    resList1 <- mts_clusterAvg(exprsMatrix = exprsMatrix, crisprMatrix = crisprMatrix, cores=cores)
    message("Running mts_InducedDependency")
    mR1 <- mts_InducedDependency(resultList=resList1, exprsMatrix=exprsMatrix, crisprMatrix=crisprMatrix, fcVal=fcVal, pVal=pVal, cores=cores)
    idGeneDepRes <- list(CRISPR_Results=data.frame(0), CRISPR_TS_Results=data.frame(0))
    idGeneDepRes[[1]] <- mR1
  } else {
    if (!is.data.frame(tissueMatrix)) {
      stop("tissueMatrix must be a data frame")
      return(NULL)
    }
    message("Running mts_clusterAvg")
    resList1 <- mts_clusterAvg(exprsMatrix = exprsMatrix, crisprMatrix = crisprMatrix, cores=cores)
    message("Running mts_InducedDependency")
    mR1 <- mts_InducedDependency(resultList=resList1, exprsMatrix=exprsMatrix, crisprMatrix=crisprMatrix, fcVal=fcVal, pVal=pVal, cores=cores)
    
    message("Running mts_CrisprTS")
    mTS1 <- mts_CrisprTS(resultList = resList1, crisprMatrix = crisprMatrix, fcVal = fcVal, pVal = pVal, tissueMatrix = tissueMatrix, allDisRes = mR1, cores=cores)
    idGeneDepRes <- list(CRISPR_Results=data.frame(0), CRISPR_TS_Results=data.frame(0))
    idGeneDepRes[[1]] <- mR1
    idGeneDepRes[[2]] <- mTS1
  }
  return(idGeneDepRes)
}