R/RNASEQ_Analysis_Duo_Trio_SVMerge_SE.r

In VilainLab/Nanotator: Next generation structural variant annotation and classification

#' Combining the RNAseq reads of family members in a
#' single file.
#'
#' @param RNASeqDir  character. Directory containing RNAseq reads.
#' @param returnMethod  character. Method of returning Data.
#' @param outpath  character. Contains file path if Method of return is chosen as
#' Text.
#' @param outFileName  character. Output file name.
#' @return Text or Dataframe containing TPM read counts of genes in the family.
#' @examples
#' \dontrun{
#' RNASeqDir = system.file("extdata", package="nanotatoR")
#' returnMethod="dataFrame"
#' datRNASeq <- RNAseqcombine(RNASeqDir = RNASeqDir,
#' returnMethod = returnMethod)
#' }
#' @importFrom stats na.omit
#' @importFrom AnnotationDbi mapIds
#' @import org.Hs.eg.db
#' @export
RNAseqcombine<-function(RNASeqDir,returnMethod=c("Text","dataFrame"),
                        outpath="",outFileName=""){
    #library(biomaRt)
    #setwd(RNASeqDir)
    l <- list.files(path = RNASeqDir,
        pattern="*.genes.results", full.names = FALSE)
    len<-length(l)
    #dat<-listDatasets(ensembl)
    #g1<-grep("sscrofa",listDatasets(ensembl)$dataset)
    'grch37 = useMart(biomart="ENSEMBL_MART_ENSEMBL", host="www.ensembl.org",
                    dataset="hsapiens_gene_ensembl")'
    gen<-c();
    ##Need to make this function dynamic
    dat<-data.frame(matrix(ncol = len,
        nrow = nrow(r<-read.table(file.path(RNASeqDir,l[1]),sep="\t",header=TRUE))))
    cnam<-c()
    for (ii in 1:length(l)){
        r <- read.table(file.path(RNASeqDir,l[ii]),sep="\t",header=TRUE)
        gen <- c(gen,as.character(r$gene_id))
        dat[,ii] <- as.numeric(r$TPM)
        str <- strsplit(l[ii],split=".genes.results")
        #print(str[[1]][1])
        cnam <- c(cnam,str[[1]][1])
    }
    #datf<-data.frame(dat)
    gen <- unique(as.character(gen))
    st <- strsplit(gen,split="[.]")
    genes <- c()
    for(k in 1:length(gen)){
        genes<-c(genes,as.character(st[[k]][1]))
    }
    data1<-dat[,1:ncol(dat)]
    names(data1)<-cnam
    genesym<-c()
    ensemblid<-c()
    'gene1 = getBM(attributes = c("external_gene_name", "ensembl_gene_id"),
                filters = "ensembl_gene_id", values = genes, mart = grch37)'
    gn1 <- mapIds(org.Hs.eg.db, genes, "SYMBOL", "ENSEMBL")
    'rn <- row.names(data.frame(gn1))
    rn1 <- row.names(data.frame(gn2))'
    gene1<-data.frame(
        ensembl_gene_id = as.character(names((gn1))),
        external_gene_name = as.character(data.frame(gn1)[,1])
    )
    genesym<-as.character(gene1$external_gene_name)
    ensemblid<-as.character(gene1$ensembl_gene_id)
    gene3<-c()
    ens<-c()
    ensemblid<-paste("^",ensemblid,"$",sep="")
    for(kk in 1:length(genes)){
        pag<-paste("^",genes[kk],"$",sep="")
        val<-grep(pag,ensemblid,fixed=TRUE)
		#if(length(val) > 1) {print(paste("val:", val, "kk:", kk))}
        if(length(val)>0){
            gene3<-c(gene3,as.character(unique(genesym[val])))
            ens<-c(ens,as.character(rep(genes[kk], length(unique(genesym[val]))
            )))
        }
        else{
            gene3<-c(gene3,as.character("-"))
            ens<-c(ens,as.character(genes[kk]))
        }
    }
    RNASeqDat<-data.frame(GeneName = as.character(gene3),
        GeneID = as.character(ens),data1)
    if(returnMethod == "Text"){
        fname = file.path(outFileName, ".csv" ,sep = "")
        write.csv(RNASeqDat,file.path(outpath,fname),
            row.names = FALSE)
    }
    else if (returnMethod == "dataFrame"){
        return (RNASeqDat)
    }
    else{
        stop("Invalid ReturnMethod")
    }
}

#' Extract Read counts for genes that overlap SVs.
#'
#' @param gnsOverlap  character. genes that overlap SV.
#' @param SVID  character. ID of the SVs.
#' @param RNASeqData  character. Expression of the genes.
#' @param pattern_Proband  character. Pattern to identify the proband reads.
#' @param pattern_Father  character. Pattern to identify the father reads.
#' @param pattern_Mother  character. Pattern to identify the mother reads.
#' @return Text or Dataframe containing TPM read counts of genes in the family.
#' @examples
#' RNASeqDir = system.file("extdata", package="nanotatoR")
#' returnMethod="dataFrame"
#' datRNASeq <- RNAseqcombine(RNASeqDir = RNASeqDir,
#' returnMethod = returnMethod)
#' gnsOverlap <- c("AGL")
#' SVID = 397
#' datgnovrlap <- OverlapRNAseq(gnsOverlap = gnsOverlap,
#' SVID = SVID, RNASeqData = datRNASeq,
#' pattern_Proband = "*_P_*")
#' @importFrom stats na.omit
#' @export
OverlapRNAseq<-function(gnsOverlap, SVID, RNASeqData,
                pattern_Proband = NA, pattern_Mother = NA,
                pattern_Father = NA){

    ###Finding the column names
    #print(gnsOverlap);print(length(gnsOverlap))
    if(is.na(unique(as.character(pattern_Father))) == FALSE){
        fatherInd<-grep(unique(as.character(pattern_Father)),names(RNASeqData))
    } else{fatherInd<- NA}
    if(is.na(unique(as.character(pattern_Mother))) == FALSE){
        motherInd<-grep(unique(as.character(pattern_Mother)),names(RNASeqData))
    } else{motherInd<- NA}
    if(is.na(unique(as.character(pattern_Proband))) == FALSE){
        probandInd<-grep(unique(as.character(pattern_Proband)),names(RNASeqData))
    } else{probandInd<- NA}
    'if(is.na(pattern_Sibling)==FALSE){
        siblingInd<-grep(pattern_Sibling,names(RNASeqData))
    }
    else{
        siblingInd<-NA
    }'
    sv<-c()
    gene<-c()
    gnsname<-as.character(RNASeqData$GeneName)
    pasgnsname<-pasgnovlap<-paste("^",gnsname,"$",sep="")
    'overlap_ensemblgenes = select(EnsDb.Hsapiens.v79, gnsOverlap,
                c("GENEID","GENENAME"), "SYMBOL")
    gnsOverlapID<-as.character(overlap_ensemblgenes$GENEID)'
    #print(paste("gnsOverlap:",gnsOverlap))
    #print(paste("overlap_ensemblgenes:",overlap_ensemblgenes))
    #print(paste("gnsOverlapID:",gnsOverlapID))
    #genes<-as.character(overlap_ensemblgenes$SYMBOL)
    ###Extracting Reads
    ###
    ###Genes Names Extraction
    #print(paste("fatherInd :",fatherInd))
    #print(paste("motherInd :",motherInd))
    #print(paste("probandInd :",probandInd))
    #print(paste("siblingInd :",siblingInd))
    gnsOverlapID <- as.character(gnsOverlap)
    #print(gnsOverlapID)
    if(length(gnsOverlapID)>1){

        datGeneInfoTemp<-data.frame()
        fatherReads<-c()
        motherReads<-c()
        probandReads<-c()
        #siblingReads<-c()
        for (ki in 1:length(gnsOverlapID)){
            pasgnovlap<-paste("^",gnsOverlapID[ki],"$",sep="")
            #print(ki)
            gg<-grep(pasgnovlap,pasgnsname,fixed=TRUE)
            dat_temp<-RNASeqData[gg,]

            if(nrow(dat_temp)>1){
                dat_temp_1<-apply(dat_temp[,3:ncol(dat_temp)],2,mean)
                #dat_temp_1<-data.frame(dat_temp_1)
                dat_temp1<-dat_temp[1,]
                dat_temp1[,3:ncol(dat_temp)]<-dat_temp_1
                 #print(dim(dat_temp1))
                fathercount<-c();mothercount<-c();
                probandcount<-c();
                if(is.na(fatherInd[1])== FALSE){
                    if(length(fatherInd)>1){
                        for(j in fatherInd){
                            fathercount<-c(fathercount,dat_temp1[,j])
                        }
                        fatherReads<-c(fatherReads,
                        paste(fathercount,collapse = ":"))
                    }else if(length(fatherInd)==1){
                        fatherReads<-c(fatherReads,dat_temp1[,fatherInd])
                    }else{
                        fatherReads<-c(fatherReads,0)
                    }
                }else{
                    fatherReads<-c(fatherReads,"-")
                }
                if(is.na(motherInd[1])==FALSE){
                    if(length(motherInd)>1){
                        for(j in motherInd){
                            mothercount<-c(mothercount,dat_temp1[,j])
                        }
                        motherReads<-c(motherReads,paste(mothercount,
                            collapse = ":"))
                    }else if(length(motherInd)==1){
                        motherReads<-c(motherReads,dat_temp1[,motherInd])
                    }else{
                        motherReads<-c(motherReads,0)
                    }
                }else{
                    motherReads<-c(motherReads,"-")
                }
                if(is.na(probandInd[1])==FALSE){
                    if(length(probandInd)>1){
                        for(j in probandInd){
                            probandcount<-c(probandcount,dat_temp1[,j])
                        }
                    probandReads<-c(probandReads,paste(probandcount,collapse=":"))
                }else if(length(probandInd)==1){
                    probandReads<-c(probandReads,dat_temp1[,probandInd])
                }else{
                    probandReads<-c(probandReads,0)
                }
                }else{
                    probandReads<-c(probandReads, "-")
                }

            'if(is.na(siblingInd[1])==FALSE){
                if(length(siblingInd)>1){
                    for(j in siblingInd){
                        siblingcount<-c(siblingcount,dat_temp1[,j])
                    }
                    siblingReads<-c(siblingReads,paste(siblingcount,collapse=":"))
                }
                else if(length(siblingInd)==1){
              siblingReads<-c(siblingReads,dat_temp1[,siblingInd])
            }
            else{
              siblingReads<-c(siblingReads,0)
            }
        }
        else{
            siblingReads<-c(siblingReads,"-")
          }'
        }
        else if (nrow(dat_temp)==1) {
          #print(dim(dat_temp1))
          fathercount<-c();mothercount<-c();probandcount<-c();
          if(is.na(fatherInd)==FALSE){
          if(length(fatherInd [1])>1){
          for(j in fatherInd){
            fathercount<-c(fathercount,mean(dat_temp[,j]))
            }
            fatherReads<-c(fatherReads,paste(fathercount,collapse=":"))
            }
            else if(length(fatherInd)==1){
            fatherReads<-c(fatherReads,mean(dat_temp[,fatherInd]))
            }
          else{
            fatherReads<-c(fatherReads,0)
            }
            }
            else{
            fatherReads<-c(fatherReads,"-")
          }
          if(is.na(motherInd [1])==FALSE){
          if(length(motherInd)>1){
          for(j in motherInd){
            mothercount<-c(mothercount,dat_temp[,j])
            }
            motherReads<-c(motherReads,paste(mothercount,collapse=":"))
            }
            else if(length(motherInd)==1){
            motherReads<-c(motherReads,mean(dat_temp[,motherInd]))
            }
          else{
            motherReads<-c(motherReads,0)
            }
            }
            else{
            motherReads<-c(motherReads, "-")
          }
           if(is.na(probandInd [1])==FALSE){
          if(length(probandInd)>1){
          for(j in probandInd){
            probandcount<-c(probandcount,dat_temp[,j])
            }
            probandReads<-c(probandReads,paste(probandcount,collapse=":"))
            }
            else if(length(probandInd)==1){
            probandReads<-c(probandReads,mean(dat_temp[,probandInd]))
            }
          else{
            probandReads<-c(probandReads,0)
            }
            }
            else{
            probandReads<-c(probandReads, "-")
          }

          'if(is.na(siblingInd[1])==FALSE){
            if(length(siblingInd)>1){
            for(j in siblingInd){
            siblingcount<-c(siblingcount,dat_temp[,j])
            }
            siblingReads<-c(siblingReads,paste(siblingcount,collapse=":"))
            }
            else if(length(siblingInd)==1){
              siblingReads<-c(siblingReads,dat_temp[,siblingInd])
            }
            else{
              siblingReads<-c(siblingReads,0)
            }
          }
          else{
            siblingReads<-c(siblingReads,"-")
          }'
        }
        else{
          fatherReads<-c(fatherReads,"-")
          motherReads<-c(motherReads,"-")
          probandReads<-c(probandReads,"-")
          'if(is.na(siblingInd[1])==FALSE){
            siblingReads<-c(siblingReads,"-")
          }
          else{
            siblingReads<-c(siblingReads,"-")
          }'
        }
        gene<-c(gene,as.character(gnsOverlapID[ki]))
    }
        if(is.na(probandInd[1])==FALSE){
            ProbandGenes<-c()
            for(ii in 1:length(gene)){
                pasgene<-paste(gene[ii],"(",probandReads[ii],")",sep="")
                ProbandGenes<-c(ProbandGenes,pasgene)
            }
            ProbandTPM<-paste(ProbandGenes,collapse=";")
        } else{
            ProbandTPM <- "-"
           }

        if(is.na(fatherInd[1])==FALSE){
            FatherGenes<-c()
            for(ii in 1:length(gene)){
                pasgene<-paste(gene[ii],"(",fatherReads[ii],")",sep="")
                FatherGenes<-c(FatherGenes,pasgene)
            }
        FatherTPM<-paste(FatherGenes,collapse=";")
        } else{
            FatherTPM <- "-"
        }
        if(is.na(motherInd[1])==FALSE){
            MotherGenes<-c()
            for(ii in 1:length(gene)){
                pasgene<-paste(gene[ii],"(",motherReads[ii],")",sep="")
                MotherGenes<-c(MotherGenes,pasgene)
            }
            MotherTPM<-paste(MotherGenes,collapse=";")
        } else{
               MotherTPM <- "-"
        }


        '        if(is.na(siblingInd[1])==FALSE){
                siblingGenes<-c()
                for(ii in 1:length(gene)){

                pasgene<-paste(gene[ii],"(",siblingReads[ii],")",sep="")
                siblingGenes<-c(siblingGenes,pasgene)
                }
                SiblingTPM<-paste(siblingGenes,collapse=";")
                }
                else{
                       SiblingTPM<-"-"
                    }
        '
        datGeneInfo<-data.frame(SVID=SVID,Probandexpression=ProbandTPM,
                Fatherexpression=FatherTPM,Motherexpression=MotherTPM)

    }
    else if(length(gnsOverlapID)==1){
       pasgnovlap<-paste("^",as.character(gnsOverlapID),"$",sep="")
        #print(ki)
        gg<-grep(pasgnovlap,pasgnsname,fixed=TRUE)
      #gg<-grep(gnsOverlapID,gnsname,fixed=TRUE)
      dat_temp<-RNASeqData[gg,]
     if(nrow(dat_temp)>1){
          dat_temp_1<-apply(dat_temp[,3:ncol(dat_temp)],2,mean)
          #dat_temp_1<-data.frame(dat_temp_1)
          dat_temp1<-dat_temp[1,]
          dat_temp1[,3:ncol(dat_temp)]<-dat_temp_1
          #dat_temp1<-cbind(dat_temp[1,1:3],dat_temp1)
           #print(dim(dat_temp1))
          fathercount<-c();mothercount<-c();probandcount<-c();
          if(is.na(fatherInd[1])==FALSE){
          if(length(fatherInd)>=1){
          for(j in fatherInd){
            fathercount<-c(fathercount,mean(dat_temp1[,j]))
            }
            fatherReads<-paste(fathercount,collapse=":")
            }
            else if(length(fatherInd)==1){
            fatherReads<-mean(dat_temp1[,fatherInd])
            }
          else{
            fatherReads<-0
            }
            } else{
            fatherReads<- "-"
            }
          if(is.na(motherInd[1])==FALSE){
          if(length(motherInd)>1){
          for(j in motherInd){
            mothercount<-c(mothercount,mean(dat_temp1[,j]))
            }
            motherReads<-paste(mothercount,collapse=":")
            }
            else if(length(motherInd)==1){
            motherReads<-mean(dat_temp1[,motherInd])
            }
          else{
            motherReads<-0
            }
            } else{
            motherReads <- "-"
            }
          if(is.na(probandInd[1])==FALSE){
          if(length(probandInd)>1){
          for(j in probandInd){
            probandcount<-c(probandcount,mean(dat_temp1[,j]))
            }
            probandReads<-paste(probandcount,collapse=":")
            }
            else if(length(probandInd)==1){
            probandReads<-mean(dat_temp1[,probandInd])
            }
          else{
            probandReads<-0
            }
            } else{
            probandReads <- "-"
            }

          'if(is.na(siblingInd[1])==FALSE){
            if(length(siblingInd)>1){
            for(j in siblingInd){
            siblingcount<-c(siblingcount,mean(dat_temp1[,j]))
            }
            siblingReads<-paste(siblingcount,collapse=":")
            }
            else if(length(siblingInd)==1){
              siblingReads<-mean(dat_temp1[,siblingInd])
            }
            else{
              siblingReads <- 0
            }
          }
          else{
                siblingReads<- "-"
          }'
        #motherReads<-dat_temp1[,motherInd]
        #probandReads<-dat_temp1[,probandInd]
        #if(is.na(siblingInd[1])==TRUE){
        #siblingReads<-"-"
        #}
        #else{
        #siblingReads<-dat_temp1[,siblingInd]
        #}
        }
      else if (nrow(dat_temp)==1){

         #print(dim(dat_temp1))
          fathercount<-c();mothercount<-c();probandcount<-c();siblingcount<-c()
          if(is.na(fatherInd[1])==FALSE){
          if(length(fatherInd)>1){
          for(j in fatherInd){
            fathercount<-c(fathercount,mean(dat_temp[,j]))
            }
            fatherReads<-paste(fathercount,collapse=":")
            }
            else if(length(fatherInd)==1){
            fatherReads<-mean(dat_temp[,fatherInd])
            }
          else{
            fatherReads<-0
            }
            }else{
                fatherReads<-"-"
            }
          if(is.na(motherInd[1])==FALSE){
          if(length(motherInd)>1){
          for(j in motherInd){
            mothercount<-c(mothercount,mean(dat_temp[,j]))
            }
            motherReads<-paste(mothercount,collapse=":")
            }
            else if(length(motherInd)==1){
            motherReads<-mean(dat_temp[,motherInd])
            }
          else{
            motherReads<-0
            }
            } else{
                motherReads<-"-"
            }
            if(is.na(probandInd [1])==FALSE){
          if(length(probandInd)>1){
          for(j in probandInd){
            probandcount<-c(probandcount,mean(dat_temp[,j]))
            }
            probandReads<-paste(probandcount,collapse=":")
            }
            else if(length(probandInd)==1){
            probandReads<-mean(dat_temp[,probandInd])
            }
          else{
            probandReads<-0
            }
            } else{
                probandReads<-"-"
            }


          'if(is.na(siblingInd[1])==FALSE){
            if(length(siblingInd)>1){
            for(j in siblingInd){
            siblingcount<-c(siblingcount,mean(dat_temp[,j]))
            }
            siblingReads<-paste(siblingcount,collapse=":")
            }
            else if(length(siblingInd)==1){
              siblingReads<-mean(dat_temp[,siblingInd])
            }
            else{
              siblingReads<-0
            }
          }
          else{
            siblingReads<-"-"
          }'
      }
      else{
        fatherReads<-"-"
        motherReads<-"-"
        probandReads<-"-"
        'if(is.na(siblingInd[1])==TRUE){
        siblingReads<-"-"
        }
        else{
        siblingReads<-"-"
        }'
      }
      #gene<-overlap_ensemblgenes$SYMBOL
      if(is.na(probandInd[1])==FALSE){
        gene<- as.character(gnsOverlapID)
        #ProbandGenes<-c()
        ProbandGenes<-paste(gene,"(",probandReads,")",sep="")
        #ProbandGenes<-c(ProbandGenes,pasgene)
        ProbandTPM<-as.character(ProbandGenes)
        }else{
            ProbandTPM <- "-"
        }
        if(is.na(fatherInd[1])==FALSE){
        FatherGenes<-paste(gene,"(",fatherReads,")",sep="")
        FatherTPM<-as.character(FatherGenes)
        }
        else{
            FatherTPM <- "-"
        }
        if(is.na(motherInd[1])==FALSE){
        MotherGenes<-paste(gene,"(",motherReads,")",sep="")
        #MotherGenes<-c(MotherGenes,pasgene)
        #}
        MotherTPM<-as.character(MotherGenes)
        }
        else{
            MotherTPM <- "-"
        }
        'if(is.na(siblingInd[1])==FALSE){
        siblingGenes<-paste(gene,"(",siblingReads,")",sep="")
        #siblingGenes<-c(siblingGenes,pasgene)
        #}
        SiblingTPM<-as.character(siblingGenes)
        }
        else{
                SiblingTPM<-"-"
        }'
        datGeneInfo<-data.frame(SVID=SVID,Probandexpression=ProbandTPM,
                Fatherexpression=FatherTPM,Motherexpression=MotherTPM)

    }
    else{
        datGeneInfo<-data.frame(SVID=SVID,Probandexpression="-",
                    Fatherexpression="-",Motherexpression="-")



    }

  #print(warnings())

  return(datGeneInfo)
}


#' Extract Read counts for genes that are near SVs.
#'
#' @param gnsNonOverlap  character. genes that are upstream
#' and/or downstream of SV.
#' @param SVID  character. ID of the SVs.
#' @param RNASeqData  character. Expression of the genes.
#' @param pattern_Proband  character. Pattern to identify the proband reads.
#' @param pattern_Father  character. Pattern to identify the father reads.
#' @param pattern_Mother  character. Pattern to identify the mother reads.
#' @return Text or Dataframe containing TPM read counts of genes in the family.
#' @examples
#' RNASeqDir = system.file("extdata", package="nanotatoR")
#' returnMethod="dataFrame"
#' datRNASeq <- RNAseqcombine(RNASeqDir = RNASeqDir,
#' returnMethod = returnMethod)
#' gnsNonOverlap <- c("DDX11L1", "MIR1302-2HG", "OR4G4P")
#' SVID = 397
#' datgnnonovrlap <- nonOverlapRNAseq(gnsNonOverlap = gnsNonOverlap,
#' SVID = SVID, RNASeqData = datRNASeq,
#' pattern_Proband = "*_P_*")
#' @importFrom stats na.omit
#' @export
nonOverlapRNAseq<-function(gnsNonOverlap,SVID,RNASeqData,
                pattern_Proband=NA,pattern_Mother=NA,
                pattern_Father=NA){
  ##Biomart annotation
  ###Checking if the input is empty; else if not empty add
  ###expression values for each genes
    datGeneInfo<-data.frame()
    SVID=SVID
    ###Extracting the index for the the parents
    if(is.na(unique(as.character(pattern_Father))) == FALSE){
        fatherInd<-grep(unique(as.character(pattern_Father)),names(RNASeqData))
    } else{fatherInd<- NA}
    if(is.na(unique(as.character(pattern_Mother))) == FALSE){
        motherInd<-grep(unique(as.character(pattern_Mother)),names(RNASeqData))
    } else{motherInd<- NA}
    if(is.na(unique(as.character(pattern_Proband))) == FALSE){
        probandInd<-grep(unique(as.character(pattern_Proband)),names(RNASeqData))
    } else{probandInd<- NA}

    ##Checking for sibling
    'if(is.na(pattern_Sibling)==FALSE){
      siblingInd<-grep(pattern_Sibling,names(RNASeqData))
    }
    else{
      siblingInd<-NA
    }'

    gene<-c()
    gnsname<-as.character(RNASeqData$GeneName)
    pasgnsname<-pasgnovlap<-paste("^",as.character(gnsname),"$",sep="")
    'nonoverlap_ensemblgenes = select(EnsDb.Hsapiens.v79, gnsNonOverlap,
                c("GENEID","GENENAME"), "SYMBOL")
    gnsnonOverlapID<-as.character(nonoverlap_ensemblgenes$GENEID)'
    ###Extracting Reads
    ###
    ###Genes Names Extraction
    gnsnonOverlapID<- as.character(gnsNonOverlap)
    if(length(gnsnonOverlapID)>1){
      #datGeneInfoTemp<-data.frame()
      fatherReads<-c()
      motherReads<-c()
      probandReads<-c()
      #siblingReads<-c()

      for (ki in 1:length(gnsnonOverlapID)){
       pasgnnonovlap<-paste("^",as.character(gnsnonOverlapID[ki]),"$",sep="")
        gg<-grep(pasgnnonovlap,pasgnsname,fixed=TRUE)
        dat_temp<-RNASeqData[gg,]
        if(nrow(dat_temp)>1){
          dat_temp_1<-apply(dat_temp[,3:ncol(dat_temp)],2,mean)
          #dat_temp_1<-data.frame(dat_temp_1)
          dat_temp1<-dat_temp[1,]
          dat_temp1[,3:ncol(dat_temp)]<-dat_temp_1
           #print(dim(dat_temp1))
          fathercount<-c();mothercount<-c();probandcount<-c();siblingcount<-c()
          if(is.na(fatherInd[1])==FALSE){
          if(length(fatherInd)>1){
          for(j in fatherInd){
            fathercount<-c(fathercount,dat_temp1[,j])
            }
            fatherReads<-c(fatherReads,paste(fathercount,collapse=":"))
            }
            else if(length(fatherInd)==1){
            fatherReads<-c(fatherReads,dat_temp1[,fatherInd])
            }
          else{
            fatherReads<-c(fatherReads,0)
            }
            }
            else{
            fatherReads<-c(fatherReads,"-")
          }
          if(is.na(motherInd[1])==FALSE){
          if(length(motherInd)>1){
          for(j in motherInd){
            mothercount<-c(mothercount,dat_temp1[,j])
            }
            motherReads<-c(motherReads,paste(mothercount,collapse=":"))
            }
            else if(length(motherInd)==1){
            motherReads<-c(motherReads,dat_temp1[,motherInd])
            }
          else{
            motherReads<-c(motherReads,0)
            }
            } else{
                motherReads<-c(motherReads, "-")
            }
          if(is.na(probandInd[1])==FALSE){
          if(length(probandInd)>1){
          for(j in probandInd){
            probandcount<-c(probandcount,dat_temp1[,j])
            }
            probandReads<-c(probandReads,paste(probandcount,collapse=":"))
            }
            else if(length(probandInd)==1){
            probandReads<-c(probandReads,dat_temp1[,probandInd])
            }
          else{
            probandReads<-c(probandReads,0)
            }
            } else{
                probandReads<-c(probandReads, "-")
            }
          'if(is.na(siblingInd[1])==FALSE){
            if(length(siblingInd)>1){
            for(j in siblingInd){
            siblingcount<-c(siblingcount,dat_temp1[,j])
            }
            siblingReads<-c(siblingReads,paste(siblingcount,collapse=":"))
            }
            else if(length(siblingInd)==1){
              siblingReads<-c(siblingReads,dat_temp1[,siblingInd])
            }
            else{
              siblingReads<-c(siblingReads,0)
            }
          }
          else{
            siblingReads<-c(siblingReads,"-")
          }'
        }
        else if (nrow(dat_temp)==1) {
          #print(dim(dat_temp1))
          fathercount<-c();mothercount<-c();probandcount<-c();
          if(is.na(fatherInd[1])==FALSE){
          if(length(fatherInd)>1){
          for(j in fatherInd){
            fathercount<-c(fathercount,dat_temp[,j])
            }
            fatherReads<-c(fatherReads,paste(fathercount,collapse=":"))
            }
            else if(length(fatherInd)==1){
            fatherReads<-c(fatherReads,dat_temp[,fatherInd])
            }
          else{
            fatherReads<-c(fatherReads,0)
            }
            }
            else{
            fatherReads<-c(fatherReads,"-")
          }

          if(is.na(motherInd[1])==FALSE){
          if(length(motherInd)>1){
          for(j in motherInd){
            mothercount<-c(mothercount,dat_temp[,j])
            }
            motherReads<-c(motherReads,paste(mothercount,collapse=":"))
            }
            else if(length(motherInd)==1){
            motherReads<-c(motherReads,dat_temp[,motherInd])
            }
          else{
            motherReads<-c(motherReads,0)
            }
         }
            else{
            motherReads<-c(motherReads,"-")
          }
           if(is.na(probandInd[1])==FALSE){
          if(length(probandInd)>1){
          for(j in probandInd){
            probandcount<-c(probandcount,dat_temp[,j])
            }
            probandReads<-c(probandReads,paste(probandcount,collapse=":"))
            }
            else if(length(probandInd)==1){
            probandReads<-c(probandReads,dat_temp[,probandInd])
            }
          else{
            probandReads<-c(probandReads,0)
            }
           }
            else{
            probandReads <- c(probandReads,"-")
          }
          'if(is.na(siblingInd[1])==FALSE){
            if(length(siblingInd)>1){
            for(j in siblingInd){
            siblingcount<-c(siblingcount,dat_temp[,j])
            }
            siblingReads<-c(siblingReads,paste(siblingcount,collapse=":"))
            }
            else if(length(siblingInd)==1){
              siblingReads<-c(siblingReads,dat_temp[,siblingInd])
            }
            else{
              siblingReads<-c(siblingReads,0)
            }
          }
          else{
            siblingReads<-c(siblingReads,"-")
          }'
        }
        else{
          fatherReads<-c(fatherReads,"-")
          motherReads<-c(motherReads,"-")
          probandReads<-c(probandReads,"-")
          'if(is.na(siblingInd[1])==FALSE){
            siblingReads<-c(siblingReads,"-")
          }
          else{
            siblingReads<-c(siblingReads,"-")
          }'
        }
        gene<-c(gene,as.character(gnsnonOverlapID[ki]))
    }
        if(is.na(probandInd[1])==FALSE){
        ProbandGenes<-c()

        for(ii in 1:length(gene)){
        pasgene<-paste(gene[ii],"(",probandReads[ii],")",sep="")
        ProbandGenes<-c(ProbandGenes,pasgene)
        }
        ProbandTPM<-paste(ProbandGenes,collapse=";")
        } else{
               ProbandTPM<-"-"
            }
         if(is.na(fatherInd[1])==FALSE){
        FatherGenes<-c()
        for(ii in 1:length(gene)){
        pasgene<-paste(gene[ii],"(",fatherReads[ii],")",sep="")
        FatherGenes<-c(FatherGenes,pasgene)
        }
        FatherTPM<-paste(FatherGenes,collapse=";")
        }else{
               FatherTPM<-"-"
            }
        if(is.na(motherInd[1])==FALSE){
        MotherGenes<-c()
        for(ii in 1:length(gene)){
        pasgene<-paste(gene[ii],"(",motherReads[ii],")",sep="")
        MotherGenes<-c(MotherGenes,pasgene)
        }
        MotherTPM<-paste(MotherGenes,collapse=";")
        }else{
               MotherTPM<-"-"
            }

        'if(is.na(siblingInd[1])==FALSE){
        siblingGenes<-c()
        for(ii in 1:length(gene)){
        pasgene<-paste(gene[ii],"(",siblingReads[ii],")",sep="")
        siblingGenes<-c(siblingGenes,pasgene)
        }
        SiblingTPM<-paste(siblingGenes,collapse=";")
        }
        else{
               SiblingTPM<-"-"
            }'
        datGeneInfo<-data.frame(SVID=SVID,ProbandTPM=ProbandTPM,
                FatherTPM=FatherTPM,MotherTPM=MotherTPM)
    }
    else if(length(gnsnonOverlapID)==1){
    pasgnnonovlap<-paste("^",as.character(gnsnonOverlapID),"$",sep="")
    gg<-grep(pasgnnonovlap,pasgnsname,fixed=TRUE)
      #gg<-grep(pasgnnonovlap,gnsname,fixed=TRUE)
      dat_temp<-RNASeqData[gg,]

      if(nrow(dat_temp)>1){
          dat_temp_1<-apply(dat_temp[,3:ncol(dat_temp)],2,mean)
          #dat_temp_1<-data.frame(dat_temp_1)
          dat_temp1<-dat_temp[1,]
          dat_temp1[,3:ncol(dat_temp)]<-dat_temp_1
           #print(dim(dat_temp1))
          fathercount<-c();mothercount<-c();probandcount<-c();
          if(is.na(fatherInd[1])==FALSE){
          if(length(fatherInd)>1){
          for(j in fatherInd){
            fathercount<-c(fathercount,dat_temp1[,j])
            }
            fatherReads<-paste(fathercount,collapse=":")
            }
            else if(length(fatherInd)==1){
            fatherReads<-dat_temp1[,fatherInd]
            }
          else{
            fatherReads<-0
            }
             }
          else{
            fatherReads<- "-"
          }
          if(is.na(motherInd[1])==FALSE){
          if(length(motherInd)>1){
          for(j in motherInd){
            mothercount<-c(mothercount,dat_temp1[,j])
            }
            motherReads<-paste(mothercount,collapse=":")
            }
            else if(length(motherInd)==1){
            motherReads<-dat_temp1[,motherInd]
            }
          else{
            motherReads<-0
            }
             }
          else{
            motherReads<- "-"
          }
          if(is.na(probandInd[1])==FALSE){
          if(length(probandInd)>1){
          for(j in probandInd){
            probandcount<-c(probandcount,dat_temp1[,j])
            }
            probandReads<-paste(probandcount,collapse=":")
            }
            else if(length(probandInd)==1){
            probandReads<-dat_temp1[,probandInd]
            }
          else{
            probandReads<-0
            }
             }
          else{
            probandReads<- "-"
          }

          'if(is.na(siblingInd[1])==FALSE){
            if(length(siblingInd)>1){
            for(j in siblingInd){
            siblingcount<-c(siblingcount,dat_temp1[,j])
            }
            siblingReads<-paste(siblingcount,collapse=":")
            }
            else if(length(siblingInd)==1){
              siblingReads<-dat_temp1[,siblingInd]
            }
            else{
              siblingReads <- 0
            }
          }
          else{
            siblingReads<- "-"
          }'
        #motherReads<-dat_temp1[,motherInd]
        #probandReads<-dat_temp1[,probandInd]
        #if(is.na(siblingInd[1])==TRUE){
        #siblingReads<-"-"
        #}
        #else{
        #siblingReads<-dat_temp1[,siblingInd]
        #}
        }
      else if (nrow(dat_temp)==1){

         #print(dim(dat_temp1))
          fathercount<-c();mothercount<-c();probandcount<-c();
          if(is.na(fatherInd[1])==FALSE){
          if(length(fatherInd)>1){
          for(j in fatherInd){
            fathercount<-c(fathercount,dat_temp[,j])
            }
            fatherReads<-paste(fathercount,collapse=":")
            }
            else if(length(fatherInd)==1){
            fatherReads<-dat_temp[,fatherInd]
            }
          else{
            fatherReads<-0
            }
            }
          else{
            fatherReads<- "-"
          }
            if(is.na(motherInd[1])==FALSE){
          if(length(motherInd)>1){
          for(j in motherInd){
            mothercount<-c(mothercount,dat_temp[,j])
            }
            motherReads<-paste(mothercount,collapse=":")
            }
            else if(length(motherInd)==1){
            motherReads<-dat_temp[,motherInd]
            }
          else{
            motherReads<-0
            }
            }
          else{
            motherReads<- "-"
          }
          if(is.na(probandInd)==FALSE){
          if(length(probandInd)>1){
          for(j in probandInd){
            probandcount<-c(probandcount,dat_temp[,j])
            }
            probandReads<-paste(probandcount,collapse=":")
            }
            else if(length(probandInd)==1){
            probandReads<-dat_temp[,probandInd]
            }
          else{
            probandReads<-0
            }
            }
          else{
            probandReads<- "-"
          }
          'if(is.na(siblingInd[1])==FALSE){
            if(length(siblingInd)>1){
            for(j in siblingInd){
            siblingcount<-c(siblingcount,dat_temp[,j])
            }
            siblingReads<-paste(siblingcount,collapse=":")
            }
            else if(length(siblingInd)==1){
              siblingReads<-dat_temp[,siblingInd]
            }
            else{
              siblingReads<-0
            }
          }
          else{
            siblingReads<-"-"
          }'
      }
      else{
        fatherReads<-"-"
        motherReads<-"-"
        probandReads<-"-"
        'if(is.na(siblingInd[1])==TRUE){
        siblingReads<-"-"
        }
        else{
        siblingReads<-"-"
        }'
      }
        gene<-c(gene,as.character(gnsnonOverlapID))
        if(is.na(probandInd[1])==FALSE){
        ProbandGenes<-c()
        ProbandGenes<-paste(gene,"(",probandReads,")",sep="")
        #ProbandGenes<-c(ProbandGenes,pasgene)
        #}
        ProbandTPM<-as.character(ProbandGenes)
        }else{
                ProbandTPM<-"-"
        }
        if(is.na(fatherInd[1])==FALSE){
        FatherGenes<-c()
        FatherGenes<-paste(gene,"(",fatherReads,")",sep="")
        FatherTPM<-as.character(FatherGenes)
        }else{
                FatherTPM <- "-"
        }
        if(is.na(motherInd[1])==FALSE){
        MotherGenes<-c()
        MotherGenes<-paste(gene,"(",motherReads,")",sep="")
        MotherTPM<-as.character(MotherGenes)
        }else{
                MotherTPM <- "-"
        }

        'if(is.na(siblingInd[1])==FALSE){
        siblingGenes<-paste(gene,"(",siblingReads,")",sep="")
        #siblingGenes<-c(siblingGenes,pasgene)
        #}
        SiblingTPM<-as.character(siblingGenes)
        }
        else{
                SiblingTPM<-"-"
        }'

        datGeneInfo<-data.frame(SVID=SVID,ProbandTPM=ProbandTPM,
                FatherTPM=FatherTPM,MotherTPM=MotherTPM)
    }
    else{
        datGeneInfo<-data.frame(SVID=SVID,ProbandTPM="-",
                FatherTPM="-",MotherTPM="-")

    }

  return(datGeneInfo)
}

#' Extract Read counts for genes that are near
#' or overalapping SVs.
#'
#' @param input_fmt_SV  character. genes that are upstream
#' and/or downstream of SV. input_fmt_RNASeq
#' @param input_fmt_RNASeq  character. input format of RNASEQ data.
#' Text or dataframe.
#' @param smapdata  dataframe. smap data in dataframe format.
#' @param smappath  character. smap path.
#' @param RNASeqPATH  character. RNASEQ path.
#' @param outputfmt  character. Output format choice dataframe or text.
#' @param RNASeqData  character. Expression of the genes.
#' @param pattern_Proband  character. Pattern to identify the proband reads.
#' @param pattern_Father  character. Pattern to identify the father reads.
#' @param pattern_Mother  character. Pattern to identify the mother reads.
#' @param EnzymeType  character. Enzyme used. option "Dual" or "DLE".
#' @return Text or Dataframe containing TPM read counts of genes in the family.
#' @examples
#' \dontrun{
#' RNASeqDir = system.file("extdata", package="nanotatoR")
#' returnMethod="dataFrame"
#' datRNASeq <- RNAseqcombine(RNASeqDir = RNASeqDir,
#' returnMethod = returnMethod)
#' smapName="NA12878_DLE1_VAP_solo5.smap"
#' smap = system.file("extdata", smapName, package="nanotatoR")
#' datcomp<-overlapnearestgeneSearch(smap = smap,
#'    bed=bedFile, inputfmtBed = "BED", outpath,
#'    n = 3, returnMethod_bedcomp = c("dataFrame"),
#'    input_fmt_SV = "Text",
#'    EnzymeType = "SVMerge",
#'    bperrorindel = 3000,
#'    bperrorinvtrans = 50000)
#' datRNASeq1 <- SVexpression(
#'     input_fmt_SV=c("dataFrame"),
#      smapdata = datcomp,
#'     input_fmt_RNASeq=c("dataFrame"),
#'     RNASeqData = datRNASeq,
#'     outputfmt=c("datFrame"),
#'     pattern_Proband = "*_P_*", EnzymeType = c("SVMerge"))

#'}
#' @importFrom stats na.omit
#' @export
SVexpression_duo_trio <-function(input_fmt_SV=c("Text","dataFrame"),
        smapdata,smappath,
        input_fmt_RNASeq=c("Text","dataFrame"),
        RNASeqData,RNASeqPATH,outputfmt=c("Text","datFrame"),
        pattern_Proband=NA,pattern_Mother=NA,pattern_Father=NA,
        EnzymeType = c("SVMerge", "SE")){
    ###RNASEQ Analysis data
    if(input_fmt_RNASeq=="dataFrame"){
      RNASeqData=RNASeqData
    }
    else if(input_fmt_RNASeq=="Text"){
      RNASeqData=read.csv(RNASeqPATH)
    }
    else{
      stop("Input format for RNASeq Data Incorrect")
    }

    if(input_fmt_SV=="dataFrame"){
        smapdata = smapdata
        if(EnzymeType == "SVMerge"){
            #smapdata <- readSMap(smap, input_fmt_smap = "Text")
            SVID<-smapdata$SVIndex
        }
        else{
            #smapdata <- readSMap_DLE(smap, input_fmt_smap)
            SVID<-smapdata$SmapEntryID
        }
    }
    else if(input_fmt_SV=="Text"){
        if(EnzymeType == "SVMerge"){
            smapdata <- readSMap(smappath, input_fmt_smap = "Text")
            SVID<-smapdata$SVIndex
        }
        else{
            smapdata <- readSMap_DLE(smappath, input_fmt_smap = "Text")
            SVID<-smapdata$SmapEntryID
        }
    }
    else{
        stop("Input format for SMAP Incorrect")
    }
    ##Extracting Data
    overlapgenes<-str_trim(smapdata$OverlapGenes_strand_perc)

    SVID<-smapdata$SVIndex
    dataOverLap<-data.frame(matrix(nrow=nrow(smapdata),ncol=4))
    ##Extracting Overlapped Genes
    #dataOverLap<-data.frame(matrix(nrow=10,ncol=5))
    names(dataOverLap)<-c("SVID","OverlapProbandTPM",
                "OverlapFatherTPM","OverlapMotherTPM")
    print("###OverlapGenes###")
    for(kk in 1:length(overlapgenes)){
        #print(kk)
        #for(kk in 1:10){
        #print(kk)
        datOverLap<-data.frame()
        print(paste("kk:",kk,sep=""))
        svID<-as.character(SVID[kk])
        if(length(grep(";",overlapgenes[kk]))>=1){
            st1<-strsplit(as.character(overlapgenes[kk]),
                split = ";")
            sttemp<-as.character(st1[[1]])
            #print("1")
            gns_overlap<-c()
            for (tt in 1:length(sttemp)){
                gn_temp<-strsplit(sttemp[tt],split="\\(")
                gns_overlap<-c(gns_overlap,as.character(gn_temp[[1]][1]))
            }

            datOverLap<-OverlapRNAseq(gnsOverlap = as.character(gns_overlap),
                SVID = svID,RNASeqData = RNASeqData,
                pattern_Proband=pattern_Proband,pattern_Mother=pattern_Mother,
                pattern_Father=pattern_Father)


        }else if (length(grep("\\(",as.character(overlapgenes[kk])))>=1){
            #print("2")
            gnsOverlap<-strsplit(as.character(overlapgenes[kk]),split="\\(")[[1]][1]

            datOverLap<-OverlapRNAseq(gnsOverlap = as.character(gnsOverlap),
                    SVID = svID,RNASeqData = RNASeqData,
                    pattern_Proband = pattern_Proband,
                    pattern_Mother = pattern_Mother,
                    pattern_Father = pattern_Father)

        }else{
        #print(paste("OverLapDNSVID:",svID))
            datOverLap<-data.frame(SVID = svID,
                Probandexpression = "-",
                Fatherexpression = "-",
                Motherexpression = "-")
        }
        dataOverLap[kk,]<-c(as.character(datOverLap$SVID),
            Proband_OverlapGeneExpression_TPM = as.character(datOverLap$Probandexpression),
            Father_OverlapGeneExpression_TPM = as.character(datOverLap$Fatherexpression),
            Mother_OverlapGeneExpression_TPM = as.character(datOverLap$Motherexpression))
    }

    ##Extracting NonOverlapped Genes
    nearestUPGenes<-smapdata$Upstream_nonOverlapGenes_dist_kb
    datanonOverLapUP<-data.frame(matrix(nrow=nrow(smapdata),ncol=4))
    names(datanonOverLapUP)<-c("SVID","NonOverlapUPProbandTPM",
                            "NonOverlapUPFatherTPM","NonOverlapUPMotherTPM")
    print("###NonOverlapUPStreamGenes###")
    for(ll in 1:length(nearestUPGenes)){
        #for(ll in 1:10){

        datNonOverLapUP<-data.frame()
        #print(paste("llUP:",ll,sep=""))
        svID<-as.character(SVID[ll])
        if(length(grep(";",nearestUPGenes[ll]))>=1){
            st1<-strsplit(as.character(nearestUPGenes[ll]),split=";")
            sttemp<-as.character(st1[[1]])
            #print("1")
            gns_nonoverlap_up<-c()
            for (mm in 1:length(sttemp)){
                gn_temp<-strsplit(sttemp[mm],split="\\(")
                gns_nonoverlap_up<-c(gns_nonoverlap_up,
                    as.character(gn_temp[[1]][1]))
            }


            datNonOverLapUP<-nonOverlapRNAseq(
                gnsNonOverlap=as.character(gns_nonoverlap_up),
                SVID=svID,RNASeqData=RNASeqData,
                pattern_Proband=pattern_Proband,
                pattern_Mother=pattern_Mother,
                pattern_Father=pattern_Father)

        }
        else if (length(grep("\\(",as.character(nearestUPGenes[ll])))>=1){
            #print("2")
            gnsNonOverlapUP<-strsplit(as.character(nearestUPGenes[ll]),split="\\(")[[1]][1]
            datNonOverLapUP<-nonOverlapRNAseq(
                gnsNonOverlap = as.character(gnsNonOverlapUP),
                SVID = svID,
                RNASeqData = RNASeqData,
                pattern_Proband = pattern_Proband,
                pattern_Mother = pattern_Mother,
                pattern_Father = pattern_Father)

        }
        else{
        #print(paste("NonOverLapUPSVID:",svID))
            datNonOverLapUP<-data.frame(SVID=svID,ProbandTPM="-",FatherTPM="-",MotherTPM="-")
                }
            datanonOverLapUP[ll,]<-c(
                as.character(datNonOverLapUP$SVID),
                Proband_Upstream_nonOverlapGeneExpression_TPM = as.character(datNonOverLapUP$ProbandTPM),
                Father_Upstream_nonOverlapGeneExpression_TPM=as.character(datNonOverLapUP$FatherTPM),
                Mother_Upstream_nonOverlapGeneExpression_TPM=as.character(datNonOverLapUP$MotherTPM))
        }

  ##Extracting NonOverlapped Down Stream Genes
    nearestDNGenes<-smapdata$Downstream_nonOverlapGenes_dist_kb
    datanonOverLapDN<-data.frame(matrix(nrow=nrow(smapdata),ncol=4))
    names(datanonOverLapDN)<-c("SVID","NonOverlapDNProbandTPM",
                            "NonOverlapDNFatherTPM","NonOverlapDNMotherTPM")
    print("###NonOverlapDNStreamGenes###")
    for(nn in 1:length(nearestDNGenes)){
    #for(nn in 1:10){
        datNonOverLapDN<-data.frame()
        # print(paste("llDN:",ll,sep=""))
        svID<-as.character(SVID[nn])
        if(length(grep(";",nearestDNGenes[nn]))>=1){
        st1<-strsplit(as.character(nearestDNGenes[nn]),split=";")
        sttemp<-as.character(st1[[1]])
        #print("1")
        gns_nonoverlap_dn<-c()
        for (mm in 1:length(sttemp)){
            gn_temp<-strsplit(sttemp[mm],split="\\(")
            gns_nonoverlap_dn<-c(gns_nonoverlap_dn,as.character(gn_temp[[1]][1]))
        }
        datNonOverLapDN<-nonOverlapRNAseq(gnsNonOverlap=as.character(gns_nonoverlap_dn),
            SVID = svID,RNASeqData = RNASeqData,
            pattern_Proband = pattern_Proband,
            pattern_Mother = pattern_Mother,
            pattern_Father=pattern_Father)

        }
        else if (length(grep("\\(",as.character(nearestDNGenes[nn])))>=1){
            # print("2")
            gnsNonOverlapDN<-strsplit(as.character(nearestDNGenes[nn]),split="\\(")[[1]][1]
            datNonOverLapDN<-nonOverlapRNAseq(
                gnsNonOverlap = as.character(gnsNonOverlapDN),
                SVID = svID,
                RNASeqData = RNASeqData,
                pattern_Proband = pattern_Proband,
                pattern_Mother = pattern_Mother,
                pattern_Father = pattern_Father)

        }
        else{
            #print(paste("NonOverLapDNSVID:",svID))
            #print ("SVID")
            datNonOverLapDN<-data.frame(SVID=svID,
                ProbandTPM = "-",
                FatherTPM="-",MotherTPM="-")
        }
        datanonOverLapDN[nn,]<-c(as.character(datNonOverLapDN$SVID),
        NonOverlapDNprobandEXP=as.character(datNonOverLapDN$ProbandTPM),
        NonOverlapDNfatherEXP=as.character(datNonOverLapDN$FatherTPM),
        NonOverlapDNmotherEXP=as.character(datNonOverLapDN$MotherTPM))
    }

    dataFinal<-data.frame(smapdata,dataOverLap[,2:ncol(dataOverLap)],
            datanonOverLapUP[,2:ncol(datanonOverLapUP)],
            datanonOverLapDN[,2:ncol(datanonOverLapDN)])
return(dataFinal)

}