R/SampleExprFun.R

In boseb/CTDPathSim2.0: Computing multi-omics driven similarity scores between patient tumor samples and cell lines for personalized medicine

#'Sample-specific deconvoluted gene expression profile.
#'
#'This is the place for description.
#'
#'Created By: Banabithi Bose| Date Created: 4/10/2022 | Stage 2 | Function 2 |
#' @param Deconv_expression A R dataframe with the deconvoluted gene expression values for each gene in constituent cell types.
#' @param Deconv_proportions A R dataframe with the estimated proportions of constituent cell types in samples.
#' @param CTDDirectory A character string for the file path of the directory for the output to be stored.
#'
#' @return R dataframes including the deconvoluted gene expression profile for each sample in the specified directory. The rows are the genes and the columns are the cell types.This function labels the columns as V1, V2, V3,....etc.
#' @export
#'
#' @examples
SampleExprFun<-function(Deconv_expression,Deconv_proportions, CTDDirectory="~"){
  library(data.table)
  if((is(Deconv_expression, "SummarizedExpirament"))){
    Deconv_expression<-assay(Deconv_expression)
  }

  if((is(Deconv_proportions, "SummarizedExpirament"))){
    Deconv_proportions<-assay(Deconv_proportions)
  }

  Deconv_expression<-abs(Deconv_expression)
  Deconv_proportions<-abs(Deconv_proportions)
  dir.create(paste0(CTDDirectory,"/Sample_expression"))##MATT TAKE CARE OF THE DIRECTORY

  processMethExp<- function(sample){
    tryCatch(
      {
        #sample=samples$V1[5]
        proportions<-Deconv_proportions[unlist(sample),]
        n1<-ncol(Deconv_expression)
        if(n1==3){
          expression<-cbind(Deconv_expression[,1]*proportions[1],Deconv_expression[,2]*proportions[2],
                            Deconv_expression[,3]*proportions[3])
        }
        if(n1==4){
          expression<-cbind(Deconv_expression[,1]*proportions[1],Deconv_expression[,2]*proportions[2],
                            Deconv_expression[,3]*proportions[3],Deconv_expression[,4]*proportions[4])
        }
        if(n1==5){
          expression<-cbind(Deconv_expression[,1]*proportions[1],Deconv_expression[,2]*proportions[2],
                            Deconv_expression[,3]*proportions[3],Deconv_expression[,4]*proportions[4],
                            Deconv_expression[,5]*proportions[5])
        }

        expression<-as.matrix(expression)
        colnames(expression)<-colnames(Deconv_expression)
        row.names(expression)<-row.names(Deconv_expression)
        save(expression,file=paste0(CTDDirectory,"/Sample_expression/",sample,".Rda"))
      }, error = function(error_condition) {
        cat(paste0(sample," : ",error_condition),file="~/sampleExprFun.txt",sep="\n",append=TRUE)
        return()
      }, finally={
      }
    )}

  samples<-data.table(row.names(Deconv_proportions))
  lapply(samples$V1,processMethExp)
  return()
}

# ##RUNNING THE FUNCTION WITH EXAMPLE DATASETS
# load("~/CTDPathSim/inst/extdata/Example.Deconv.expression.rda")
# load("~/CTDPathSim/inst/extdata/Example.Deconv.proportions.450K.rda")
# ##SAMPLE SPECIFIC EXPRESSION FILES ARE SAVED IN Sample_expression FOLDER
# SampleExprFun(Deconv_expression,Deconv_proportions)