R/mts_GeneDepMutation.R

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

mts_GeneDepMutation = function(exprsMatrix = exprsMatrix, mutMatrix = mutMatrix, cores = cores, 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(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(mutMatrix))
  {
    stop("No Mutation Matrix Provided")
  } else {
    if (!is.data.frame(mutMatrix)) {
      stop("mutMatrix must be a data frame")
      return(NULL)
    }
  }
  
  if(missing(tissueMatrix))
  {
    stop("No Tissue Matrix Provided")
  } else {
    if (!is.data.frame(tissueMatrix)) {
      stop("tissueMatrix must be a data frame")
      return(NULL)
    }
  }
  
  message("Running mts_mixModelCluster")
  resList1 <- mts_mixModelCluster(dataMatrix = exprsMatrix, cores=cores)
  message("Running mts_Mutation")
  mMut1 <- mts_Mutation(resultList = resList1, tissueMatrix = tissueMatrix, mutMatrix=mutMatrix, cores=cores, pVal=pVal)
  colnames(mMut1) <- c("mRNA_Gene", "mutation_gene", "tissue", "pvalue", "mMode")
  return(mMut1)
}