Bhattacharya authored on 20/08/2021 20:18:52 | 1 | 1 |
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+#' Combining the RNAseq reads of family members in a |
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+#' single file. |
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+#' |
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+#' @param RNASeqDir character. Directory containing RNAseq reads. |
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+#' @param returnMethod character. Method of returning Data. |
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+#' @param outpath character. Contains file path if Method of return is chosen as |
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+#' Text. |
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+#' @param outFileName character. Output file name. |
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+#' @return Text or Dataframe containing TPM read counts of genes in the family. |
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+#' @examples |
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+#' RNASeqDir = system.file("extdata", package="nanotatoR")
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+#' returnMethod="dataFrame" |
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+#' datRNASeq <- RNAseqcombine_solo(RNASeqDir = RNASeqDir, |
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+#' returnMethod = returnMethod) |
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+#' @importFrom AnnotationDbi mapIds |
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+#' @importFrom stats na.omit |
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+#' @import org.Hs.eg.db |
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+#' @export |
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+RNAseqcombine_solo<-function(RNASeqDir,returnMethod=c("Text","dataFrame"),
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+ outpath="",outFileName=""){
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+ #library() |
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+ #setwd(RNASeqDir) |
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+ l <- list.files(path = RNASeqDir, |
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+ pattern="*.genes.results", full.names = TRUE) |
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+ len<-length(l) |
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+ #dat<-listDatasets(ensembl) |
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+ #g1<-grep("sscrofa",listDatasets(ensembl)$dataset)
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+ 'grch37 = useMart(="ENSEMBL_MART_ENSEMBL", host="www.ensembl.org", |
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+ dataset="hsapiens_gene_ensembl")' |
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+ gen<-c(); |
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+ ##Need to make this function dynamic |
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+ dat<-data.frame(matrix(ncol=len,nrow=nrow(r<-read.table(l[1],sep="\t",header=TRUE)))) |
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+ cnam<-c() |
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+ for (ii in 1:length(l)){
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+ r<-read.table(l[ii],sep="\t",header=TRUE) |
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+ gen<-c(gen,as.character(r$gene_id)) |
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+ dat[,ii]<-as.numeric(r$TPM) |
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+ str<-strsplit(l[ii],split=".genes.results") |
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+ #print(str[[1]][1]) |
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+ cnam<-c(cnam,str[[1]][1]) |
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+ } |
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+ #datf<-data.frame(dat) |
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+ gen<-unique(as.character(gen)) |
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+ st<-strsplit(gen,split="[.]") |
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+ genes<-c() |
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+ for(k in 1:length(gen)){
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+ genes<-c(genes,as.character(st[[k]][1])) |
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+ } |
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+ data1 <- data.frame(dat[,1]) |
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+ names(data1) <- cnam |
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+ genesym <- c() |
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+ ensemblid <- c() |
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+ 'gene1 = getBM(attributes = c("external_gene_name", "ensembl_gene_id"),
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+ filters = "ensembl_gene_id", values = genes, mart = grch37)' |
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+ gn1 <- mapIds(org.Hs.eg.db, genes, "SYMBOL", "ENSEMBL") |
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+ 'rn <- row.names(data.frame(gn1)) |
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+ rn1 <- row.names(data.frame(gn2))' |
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+ gene1<-data.frame( |
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+ ensembl_gene_id = as.character(names((gn1))), |
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+ external_gene_name = as.character(data.frame(gn1)[,1]) |
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+ ) |
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+ genesym<-as.character(gene1$external_gene_name) |
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+ ensemblid<-as.character(gene1$ensembl_gene_id) |
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+ gene3<-c() |
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+ ens<-c() |
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+ ensemblid<-paste("^",ensemblid,"$",sep="")
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+ for(kk in 1:length(genes)){
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+ pag<-paste("^",genes[kk],"$",sep="")
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+ val<-grep(pag,ensemblid,fixed=TRUE) |
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+ if(length(val)>0){
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+ gene3<-c(gene3,as.character(unique(genesym[val]))) |
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+ ens<-c(ens,as.character(genes[kk])) |
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+ } |
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+ else{
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+ gene3<-c(gene3,as.character("-"))
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+ ens<-c(ens,as.character(genes[kk])) |
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+ } |
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+ } |
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+ RNASeqDat<-data.frame(GeneName = as.character(gene3), |
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+ GeneID = as.character(ens),data1) |
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+ if(returnMethod=="Text"){
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+ fname = file.path(outFileName,".csv",sep = "") |
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+ write.csv(RNASeqDat,file.path(outpath,fname), row.names = FALSE ) |
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+ } |
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+ else if (returnMethod=="dataFrame"){
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+ return (RNASeqDat) |
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+ } |
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+ else{
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+ stop("Invalid ReturnMethod")
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+ } |
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+} |
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+#' Annotating the Overlapping genes with RNAseq expression |
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+#' |
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+#' @param gnsOverlap character. Vector containing overlapping genes. |
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+#' @param SVID character. SV Index ID. |
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+#' @param RNASeqData dataFrame. RNAseq data with gene names. |
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+#' @param pattern_Proband character. Pattern for proband. |
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+#' @return Dataframe containing TPM read counts of overlapping genes. |
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+#' @examples |
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+#' RNASeqDir = system.file("extdata", package="nanotatoR")
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+#' returnMethod="dataFrame" |
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+#' datRNASeq <- RNAseqcombine_solo(RNASeqDir = RNASeqDir, |
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+#' returnMethod = returnMethod) |
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+#' gnsOverlap <- c("AGL")
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+#' SVID = 397 |
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+#' datgnovrlap <- OverlapRNAseq_solo(gnsOverlap = gnsOverlap, |
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+#' SVID = SVID, RNASeqData = datRNASeq, |
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+#' pattern_Proband = "*_P_*") |
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+#' @importFrom stats na.omit |
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+#' @export |
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+OverlapRNAseq_solo<-function(gnsOverlap, SVID, RNASeqData, |
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+ pattern_Proband = NA){
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+ |
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+ ###Finding the column names |
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+ #print(gnsOverlap);print(length(gnsOverlap)) |
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+ 'if(is.na(pattern_Father)==FALSE){
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+ fatherInd<-grep(pattern_Father,names(RNASeqData)) |
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+ } else{fatherInd<- NA}
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+ if(is.na(pattern_Mother)==FALSE){
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+ motherInd<-grep(pattern_Mother,names(RNASeqData)) |
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+ } else{motherInd<- NA}'
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+ if(is.na(pattern_Proband)==FALSE){
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+ probandInd <- grep(pattern_Proband,names(RNASeqData)) |
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+ } else{probandInd<- NA}
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+ 'if(is.na(pattern_Sibling)==FALSE){
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+ siblingInd<-grep(pattern_Sibling,names(RNASeqData)) |
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+ } |
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+ else{
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+ siblingInd<-NA |
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+ }' |
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+ sv<-c() |
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+ gene<-c() |
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+ gnsname<-as.character(RNASeqData$GeneName) |
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+ pasgnsname<-pasgnovlap<-paste("^",gnsname,"$",sep="")
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+ 'overlap_ensemblgenes = select(EnsDb.Hsapiens.v79, gnsOverlap, |
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+ c("GENEID","GENENAME"), "SYMBOL")
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+ gnsOverlapID<-as.character(overlap_ensemblgenes$GENEID)' |
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+ #print(paste("gnsOverlap:",gnsOverlap))
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+ #print(paste("overlap_ensemblgenes:",overlap_ensemblgenes))
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+ #print(paste("gnsOverlapID:",gnsOverlapID))
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+ #genes<-as.character(overlap_ensemblgenes$SYMBOL) |
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+ ###Extracting Reads |
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+ ### |
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+ ###Genes Names Extraction |
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+ #print(paste("fatherInd :",fatherInd))
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+ #print(paste("motherInd :",motherInd))
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+ #print(paste("probandInd :",probandInd))
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+ #print(paste("siblingInd :",siblingInd))
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+ gnsOverlapID <- as.character(gnsOverlap) |
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+ #print(gnsOverlapID) |
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+ if(length(gnsOverlapID)>1){
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+ |
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+ datGeneInfoTemp<-data.frame() |
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+ fatherReads<-c() |
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+ motherReads<-c() |
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+ probandReads<-c() |
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+ siblingReads<-c() |
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+ for (ki in 1:length(gnsOverlapID)){
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+ pasgnovlap <- paste("^", gnsOverlapID[ki],"$", sep = "")
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+ #print(ki) |
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+ gg<-grep(pasgnovlap, pasgnsname, fixed = TRUE) |
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+ dat_temp<-RNASeqData[gg, ] |
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+ |
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+ if(nrow(dat_temp)>1){
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+ #print("FALSE")
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+ #print(ki) |
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+ dat_temp_1 <- mean(dat_temp[,probandInd]) |
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+ #dat_temp_1<-data.frame(dat_temp_1) |
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+ dat_temp1 <- dat_temp[1,] |
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+ dat_temp1[,probandInd] <- dat_temp_1 |
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+ #print(dim(dat_temp1)) |
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+ |
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+ if(is.na(probandInd[1])==FALSE){
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+ if(length(probandInd)>1){
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+ for(j in probandInd){
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+ probandcount<-c(probandcount,dat_temp1[,j]) |
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+ } |
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+ probandReads<-c( |
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+ probandReads,paste(probandcount,collapse = ":")) |
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+ } |
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+ else if(length(probandInd)==1){
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+ probandReads<-c(probandReads,dat_temp1[,probandInd]) |
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+ } |
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+ else{
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+ probandReads<-c(probandReads,0) |
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+ } |
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+ } |
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+ else{
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+ probandReads<-c(probandReads,"-") |
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+ } |
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+ } |
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+ else if (nrow(dat_temp)==1) {
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+ #print("TRUE")
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+ #print(dim(dat_temp1)) |
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+ probandcount<-c() |
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+ if(is.na(probandInd [1])==FALSE){
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+ if(length(probandInd)>1){
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+ for(j in probandInd){
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+ probandcount<-c(probandcount,dat_temp[,j]) |
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+ } |
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+ probandReads<-c( |
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+ probandReads, paste(probandcount,collapse = ":")) |
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+ } |
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+ else if(length(probandInd)==1){
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+ probandReads<-c( |
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+ probandReads, mean(dat_temp[,probandInd])) |
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+ } |
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+ else{
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+ probandReads<-c(probandReads,0) |
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+ } |
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+ } |
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+ else{
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+ probandReads<-c(probandReads, "-") |
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+ } |
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+ } |
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+ else{
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+ probandReads<-c(probandReads,"-") |
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+ } |
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+ gene<-c(gene,as.character(gnsOverlapID[ki])) |
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+ } |
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+ if(is.na(probandInd[1])==FALSE){
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+ ProbandGenes<-c() |
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+ for(ii in 1:length(gene)){
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+ pasgene<-paste(gene[ii],"(", probandReads[ii],")", sep = "")
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+ ProbandGenes<-c(ProbandGenes,pasgene) |
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+ } |
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+ ProbandTPM<-paste(ProbandGenes,collapse=";") |
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+ } else{
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+ ProbandTPM <- "-" |
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+ } |
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+ datGeneInfo<-data.frame(SVID=SVID, ProbandTPM=ProbandTPM) |
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+ |
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+ } |
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+ else if(length(gnsOverlapID)==1){
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+ pasgnovlap<-paste("^",as.character(gnsOverlapID),"$",sep="")
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+ #print(ki) |
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+ gg<-grep(pasgnovlap,pasgnsname,fixed=TRUE) |
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+ |
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+ dat_temp<-RNASeqData[gg,] |
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+ if(nrow(dat_temp)>1){
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+ dat_temp_1 <- mean(dat_temp[,probandInd]) |
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+ #dat_temp_1<-data.frame(dat_temp_1) |
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+ dat_temp1<-dat_temp[1,] |
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+ dat_temp1[,probandInd]<-dat_temp_1 |
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+ #dat_temp1<-cbind(dat_temp[1,1:3],dat_temp1) |
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+ #print(dim(dat_temp1)) |
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+ probandcount<-c() |
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+ if(is.na(probandInd[1])==FALSE){
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+ if(length(probandInd)>1){
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+ for(j in probandInd){
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+ probandcount <- c(probandcount,mean(dat_temp1[,j])) |
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+ } |
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+ probandReads <- paste(probandcount,collapse = ":") |
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+ } |
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+ else if(length(probandInd)==1){
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+ probandReads<-mean(dat_temp1[,probandInd]) |
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+ } |
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+ else{
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+ probandReads <- 0 |
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+ } |
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+ } |
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+ else{
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+ probandReads <- "-" |
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+ } |
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+ |
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+ |
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+ #motherReads<-dat_temp1[,motherInd] |
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+ #probandReads<-dat_temp1[,probandInd] |
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+ #if(is.na(siblingInd[1])==TRUE){
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+ #siblingReads<-"-" |
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+ #} |
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+ #else{
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+ #siblingReads<-dat_temp1[,siblingInd] |
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+ #} |
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+ } |
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+ else if (nrow(dat_temp)==1){
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+ |
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+ #print(dim(dat_temp1)) |
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+ if(is.na(probandInd[1])==FALSE){
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+ if(length(probandInd)>1){
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+ for(j in probandInd){
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+ probandcount <- c(probandcount,mean(dat_temp[,j])) |
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+ } |
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+ probandReads<-paste(probandcount,collapse=":") |
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+ } |
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+ else if(length(probandInd)==1){
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+ probandReads<-mean(dat_temp[,probandInd]) |
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+ } |
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+ else{
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+ probandReads<-0 |
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+ } |
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+ } else{
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+ probandReads<-"-" |
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+ } |
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+ } |
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+ else{
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+ probandReads<-"-" |
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+ } |
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+ #gene<-overlap_ensemblgenes$SYMBOL |
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+ if(is.na(probandInd[1])==FALSE){
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+ gene<- as.character(gnsOverlapID) |
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+ |
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+ ProbandGenes<-paste(gene,"(",probandReads,")",sep="")
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+ #ProbandGenes<-c(ProbandGenes,pasgene) |
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+ ProbandTPM<-as.character(ProbandGenes) |
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+ }else{
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+ ProbandTPM <- "-" |
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+ } |
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+ datGeneInfo<-data.frame(SVID = SVID,ProbandTPM = ProbandTPM) |
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+ |
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+ } |
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+ else{
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+ datGeneInfo <- data.frame(SVID = SVID,ProbandTPM = "-") |
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+ } |
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+ |
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+ #print(warnings()) |
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+ |
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+ return(datGeneInfo) |
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+} |
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+#' Annotating the Non-Overlapping genes with RNAseq expression |
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+#' |
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+#' @param gnsNonOverlap character. Vector containing non-overlapping genes. |
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| 323 |
+#' @param SVID character. SV Index ID. |
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| 324 |
+#' @param RNASeqData dataFrame. RNAseq data with gene names. |
|
| 325 |
+#' @param pattern_Proband character. Pattern for proband. |
|
| 326 |
+#' @return Dataframe containing TPM read counts of overlapping genes. |
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| 327 |
+#' @examples |
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| 328 |
+#' RNASeqDir = system.file("extdata", package="nanotatoR")
|
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| 329 |
+#' returnMethod="dataFrame" |
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| 330 |
+#' datRNASeq <- RNAseqcombine_solo(RNASeqDir = RNASeqDir, |
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| 331 |
+#' returnMethod = returnMethod) |
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| 332 |
+#' gnsNonOverlap <- c("DDX11L1", "MIR1302-2HG", "OR4G4P")
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| 333 |
+#' SVID = 397 |
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| 334 |
+#' datgnnonovrlap <- nonOverlapRNAseq_solo(gnsNonOverlap = gnsNonOverlap, |
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| 335 |
+#' SVID = SVID, RNASeqData = datRNASeq, |
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| 336 |
+#' pattern_Proband = "*_P_*") |
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| 337 |
+#' @importFrom stats na.omit |
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| 338 |
+#' @export |
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| 339 |
+ |
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| 340 |
+nonOverlapRNAseq_solo<-function(gnsNonOverlap,SVID,RNASeqData, |
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+ pattern_Proband = NA){
|
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| 342 |
+ ## annotation |
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| 343 |
+ ###Checking if the input is empty; else if not empty add |
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+ ###expression values for each genes |
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| 345 |
+ datGeneInfo<-data.frame() |
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+ SVID=SVID |
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| 347 |
+ ###Extracting the index for the the parents |
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| 348 |
+ 'if(is.na(pattern_Father)==FALSE){
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| 349 |
+ fatherInd<-grep(pattern_Father,names(RNASeqData)) |
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| 350 |
+ } else{fatherInd <- NA}
|
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| 351 |
+ if(is.na(pattern_Mother)==FALSE){
|
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+ motherInd<-grep(pattern_Mother,names(RNASeqData)) |
|
| 353 |
+ } else{motherInd <- NA}'
|
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| 354 |
+ if(is.na(pattern_Proband)==FALSE){
|
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| 355 |
+ probandInd<-grep(pattern_Proband,names(RNASeqData)) |
|
| 356 |
+ } else{probandInd <- NA}
|
|
| 357 |
+ ##Checking for sibling |
|
| 358 |
+ 'if(is.na(pattern_Sibling)==FALSE){
|
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| 359 |
+ siblingInd<-grep(pattern_Sibling,names(RNASeqData)) |
|
| 360 |
+ } |
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| 361 |
+ else{
|
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+ siblingInd<-NA |
|
| 363 |
+ }' |
|
| 364 |
+ |
|
| 365 |
+ gene<-c() |
|
| 366 |
+ gnsname<-as.character(RNASeqData$GeneName) |
|
| 367 |
+ pasgnsname<-pasgnovlap<-paste("^",as.character(gnsname),"$",sep="")
|
|
| 368 |
+ 'nonoverlap_ensemblgenes = select(EnsDb.Hsapiens.v79, gnsNonOverlap, |
|
| 369 |
+ c("GENEID","GENENAME"), "SYMBOL")
|
|
| 370 |
+ gnsnonOverlapID<-as.character(nonoverlap_ensemblgenes$GENEID)' |
|
| 371 |
+ ###Extracting Reads |
|
| 372 |
+ ### |
|
| 373 |
+ ###Genes Names Extraction |
|
| 374 |
+ gnsnonOverlapID<- as.character(gnsNonOverlap) |
|
| 375 |
+ if(length(gnsnonOverlapID)>1){
|
|
| 376 |
+ #datGeneInfoTemp<-data.frame() |
|
| 377 |
+ probandReads<-c() |
|
| 378 |
+ |
|
| 379 |
+ |
|
| 380 |
+ for (ki in 1:length(gnsnonOverlapID)){
|
|
| 381 |
+ |
|
| 382 |
+ pasgnnonovlap <- paste("^",as.character(
|
|
| 383 |
+ gnsnonOverlapID[ki]),"$",sep = "") |
|
| 384 |
+ gg<-grep(pasgnnonovlap,pasgnsname,fixed=TRUE) |
|
| 385 |
+ dat_temp<-RNASeqData[gg,] |
|
| 386 |
+ if(nrow(dat_temp)>1){
|
|
| 387 |
+ dat_temp_1 <- mean(dat_temp[,probandInd]) |
|
| 388 |
+ #dat_temp_1<-data.frame(dat_temp_1) |
|
| 389 |
+ dat_temp1<-dat_temp[1,] |
|
| 390 |
+ dat_temp1[,probandInd]<-dat_temp_1 |
|
| 391 |
+ #print(dim(dat_temp1)) |
|
| 392 |
+ probandcount<-c() |
|
| 393 |
+ if(is.na(probandInd[1]) == FALSE){
|
|
| 394 |
+ if(length(probandInd)>1){
|
|
| 395 |
+ for(j in probandInd){
|
|
| 396 |
+ probandcount <- c(probandcount,dat_temp1[,j]) |
|
| 397 |
+ } |
|
| 398 |
+ probandReads<-c( |
|
| 399 |
+ probandReads,paste(probandcount,collapse=":") |
|
| 400 |
+ ) |
|
| 401 |
+ } |
|
| 402 |
+ else if(length(probandInd)==1){
|
|
| 403 |
+ probandReads<-c(probandReads,dat_temp1[,probandInd]) |
|
| 404 |
+ } |
|
| 405 |
+ else{
|
|
| 406 |
+ probandReads<-c(probandReads,0) |
|
| 407 |
+ } |
|
| 408 |
+ } else{
|
|
| 409 |
+ probandReads<-c(probandReads, "-") |
|
| 410 |
+ } |
|
| 411 |
+ } |
|
| 412 |
+ else if (nrow(dat_temp)==1) {
|
|
| 413 |
+ #print(dim(dat_temp1)) |
|
| 414 |
+ probandcount<-c() |
|
| 415 |
+ if(is.na(probandInd[1]) == FALSE){
|
|
| 416 |
+ if(length(probandInd)>1){
|
|
| 417 |
+ for(j in probandInd){
|
|
| 418 |
+ probandcount <- c(probandcount, dat_temp[,j]) |
|
| 419 |
+ } |
|
| 420 |
+ probandReads<-c(probandReads,paste(probandcount,collapse=":")) |
|
| 421 |
+ } |
|
| 422 |
+ else if(length(probandInd)==1){
|
|
| 423 |
+ probandReads<-c(probandReads,dat_temp[,probandInd]) |
|
| 424 |
+ } |
|
| 425 |
+ else{
|
|
| 426 |
+ probandReads<-c(probandReads,0) |
|
| 427 |
+ } |
|
| 428 |
+ } |
|
| 429 |
+ else{
|
|
| 430 |
+ probandReads <- c(probandReads,"-") |
|
| 431 |
+ } |
|
| 432 |
+ } |
|
| 433 |
+ else{
|
|
| 434 |
+ probandReads<-c(probandReads,"-") |
|
| 435 |
+ } |
|
| 436 |
+ gene<-c(gene,as.character(gnsnonOverlapID[ki])) |
|
| 437 |
+ } |
|
| 438 |
+ if(is.na(probandInd[1])==FALSE){
|
|
| 439 |
+ ProbandGenes<-c() |
|
| 440 |
+ |
|
| 441 |
+ for(ii in 1:length(gene)){
|
|
| 442 |
+ pasgene<-paste(gene[ii],"(",probandReads[ii],")",sep="")
|
|
| 443 |
+ ProbandGenes<-c(ProbandGenes,pasgene) |
|
| 444 |
+ } |
|
| 445 |
+ ProbandTPM<-paste(ProbandGenes,collapse=";") |
|
| 446 |
+ } else{
|
|
| 447 |
+ ProbandTPM<-"-" |
|
| 448 |
+ } |
|
| 449 |
+ datGeneInfo<-data.frame(SVID=SVID,ProbandTPM=ProbandTPM) |
|
| 450 |
+ } |
|
| 451 |
+ else if(length(gnsnonOverlapID)==1){
|
|
| 452 |
+ pasgnnonovlap<-paste("^",as.character(gnsnonOverlapID),"$",sep="")
|
|
| 453 |
+ gg<-grep(pasgnnonovlap,pasgnsname,fixed=TRUE) |
|
| 454 |
+ #gg<-grep(pasgnnonovlap,gnsname,fixed=TRUE) |
|
| 455 |
+ dat_temp<-RNASeqData[gg,] |
|
| 456 |
+ |
|
| 457 |
+ if(nrow(dat_temp)>1){
|
|
| 458 |
+ dat_temp_1 <- mean(dat_temp[,probandInd]) |
|
| 459 |
+ #dat_temp_1<-data.frame(dat_temp_1) |
|
| 460 |
+ dat_temp1<-dat_temp[1,] |
|
| 461 |
+ dat_temp1[, probandInd]<-dat_temp_1 |
|
| 462 |
+ #print(dim(dat_temp1)) |
|
| 463 |
+ probandcount<-c() |
|
| 464 |
+ if(is.na(probandInd[1])==FALSE){
|
|
| 465 |
+ if(length(probandInd)>1){
|
|
| 466 |
+ for(j in probandInd){
|
|
| 467 |
+ probandcount<-c(probandcount,dat_temp1[,j]) |
|
| 468 |
+ } |
|
| 469 |
+ probandReads<-paste(probandcount,collapse=":") |
|
| 470 |
+ } |
|
| 471 |
+ else if(length(probandInd)==1){
|
|
| 472 |
+ probandReads<-dat_temp1[,probandInd] |
|
| 473 |
+ } |
|
| 474 |
+ else{
|
|
| 475 |
+ probandReads<-0 |
|
| 476 |
+ } |
|
| 477 |
+ } |
|
| 478 |
+ else{
|
|
| 479 |
+ probandReads<- "-" |
|
| 480 |
+ } |
|
| 481 |
+ |
|
| 482 |
+ |
|
| 483 |
+ } |
|
| 484 |
+ else if (nrow(dat_temp)==1){
|
|
| 485 |
+ |
|
| 486 |
+ #print(dim(dat_temp1)) |
|
| 487 |
+ probandcount<-c() |
|
| 488 |
+ if(is.na(probandInd)==FALSE){
|
|
| 489 |
+ if(length(probandInd)>1){
|
|
| 490 |
+ for(j in probandInd){
|
|
| 491 |
+ probandcount<-c(probandcount,dat_temp[,j]) |
|
| 492 |
+ } |
|
| 493 |
+ probandReads <- paste(probandcount,collapse=":") |
|
| 494 |
+ } |
|
| 495 |
+ else if(length(probandInd)==1){
|
|
| 496 |
+ probandReads <- dat_temp[,probandInd] |
|
| 497 |
+ } |
|
| 498 |
+ else{
|
|
| 499 |
+ probandReads<-0 |
|
| 500 |
+ } |
|
| 501 |
+ } |
|
| 502 |
+ else{
|
|
| 503 |
+ probandReads<- "-" |
|
| 504 |
+ } |
|
| 505 |
+ } |
|
| 506 |
+ else{
|
|
| 507 |
+ probandReads<-"-" |
|
| 508 |
+ } |
|
| 509 |
+ gene<-c(gene,as.character(gnsnonOverlapID)) |
|
| 510 |
+ if(is.na(probandInd[1])==FALSE){
|
|
| 511 |
+ ProbandGenes <- c() |
|
| 512 |
+ ProbandGenes <- paste(gene,"(",probandReads,")",sep="")
|
|
| 513 |
+ #ProbandGenes<-c(ProbandGenes,pasgene) |
|
| 514 |
+ #} |
|
| 515 |
+ ProbandTPM<-as.character(ProbandGenes) |
|
| 516 |
+ }else{
|
|
| 517 |
+ ProbandTPM<-"-" |
|
| 518 |
+ } |
|
| 519 |
+ datGeneInfo <- data.frame(SVID = SVID,ProbandTPM = ProbandTPM) |
|
| 520 |
+ } |
|
| 521 |
+ else{
|
|
| 522 |
+ datGeneInfo < -data.frame(SVID = SVID,ProbandTPM = "-") |
|
| 523 |
+ |
|
| 524 |
+ } |
|
| 525 |
+ return(datGeneInfo) |
|
| 526 |
+} |
|
| 527 |
+#' Annotating the Overlapping and Non-Overlapping genes with RNAseq expression |
|
| 528 |
+#' |
|
| 529 |
+#' @param input_fmt_SV character. Input format of the SV data.Options |
|
| 530 |
+#' "Text" or "DataFrame". |
|
| 531 |
+#' @param smapdata dataframe. SV data dataframe. |
|
| 532 |
+#' @param smappath character. smap path. |
|
| 533 |
+#' @param input_fmt_RNASeq character. Input format of |
|
| 534 |
+#' the RNASeq data. Options "Text" or "DataFrame".. |
|
| 535 |
+#' @param RNASeqData dataFrame. RNAseq data with gene names. |
|
| 536 |
+#' @param RNASeqPATH character. RNAseq dataset path . |
|
| 537 |
+#' @param outputfmt character. Output format of |
|
| 538 |
+#' the result. Options "Text" or "DataFrame".. |
|
| 539 |
+#' @param pattern_Proband character. Pattern for proband. |
|
| 540 |
+#' @param EnzymeType character. Enzyme used. option "SVMerge" or "SE". |
|
| 541 |
+#' @return Dataframe Annotated datafreme with RNASeq data. |
|
| 542 |
+#' @examples |
|
| 543 |
+#' RNASeqDir = system.file("extdata", package="nanotatoR")
|
|
| 544 |
+#' returnMethod="dataFrame" |
|
| 545 |
+#' datRNASeq <- RNAseqcombine_solo(RNASeqDir = RNASeqDir, |
|
| 546 |
+#' returnMethod = returnMethod) |
|
| 547 |
+#' smapName="NA12878_DLE1_VAP_solo5.smap" |
|
| 548 |
+#' smap = system.file("extdata", smapName, package="nanotatoR")
|
|
| 549 |
+#' smap = system.file("extdata", smapName, package="nanotatoR")
|
|
| 550 |
+#' bedFile <- system.file("extdata", "HomoSapienGRCH19_lift37.bed", package="nanotatoR")
|
|
| 551 |
+#' outpath <- system.file("extdata", package="nanotatoR")
|
|
| 552 |
+#' datcomp<-overlapnearestgeneSearch(smap = smap, |
|
| 553 |
+#' bed=bedFile, inputfmtBed = "bed", outpath, |
|
| 554 |
+#' n = 3, returnMethod_bedcomp = c("dataFrame"),
|
|
| 555 |
+#' input_fmt_SV = "Text", |
|
| 556 |
+#' EnzymeType = "SE", |
|
| 557 |
+#' bperrorindel = 3000, |
|
| 558 |
+#' bperrorinvtrans = 50000) |
|
| 559 |
+#' datRNASeq1 <- SVexpression_solo (input_fmt_SV=c("dataFrame"),
|
|
| 560 |
+#' smapdata = datcomp, |
|
| 561 |
+#' input_fmt_RNASeq=c("dataFrame"),
|
|
| 562 |
+#' RNASeqData = datRNASeq, |
|
| 563 |
+#' outputfmt=c("datFrame"),
|
|
| 564 |
+#' pattern_Proband = "*_P_*", EnzymeType = c("SE"))
|
|
| 565 |
+#' datRNASeq1[1,] |
|
| 566 |
+#' @importFrom stats na.omit |
|
| 567 |
+#' @export |
|
| 568 |
+SVexpression_solo <- function(input_fmt_SV=c("Text","dataFrame"),
|
|
| 569 |
+ smapdata,smappath, input_fmt_RNASeq=c("Text","dataFrame"),
|
|
| 570 |
+ RNASeqData,RNASeqPATH,outputfmt=c("Text","datFrame"),
|
|
| 571 |
+ pattern_Proband = NA, EnzymeType = c("SVMerge", "SE")){
|
|
| 572 |
+ ###RNASEQ Analysis data |
|
| 573 |
+ if(input_fmt_RNASeq=="dataFrame"){
|
|
| 574 |
+ RNASeqData = RNASeqData |
|
| 575 |
+ } |
|
| 576 |
+ else if(input_fmt_RNASeq=="Text"){
|
|
| 577 |
+ RNASeqData=read.csv(RNASeqPATH) |
|
| 578 |
+ } |
|
| 579 |
+ else{
|
|
| 580 |
+ stop("Input format for RNASeq Data Incorrect")
|
|
| 581 |
+ } |
|
| 582 |
+ |
|
| 583 |
+ if(input_fmt_SV=="dataFrame"){
|
|
| 584 |
+ smapdata = smapdata |
|
| 585 |
+ if(EnzymeType == "SVMerge"){
|
|
| 586 |
+ #smapdata <- readSMap(smap, input_fmt_smap = "Text") |
|
| 587 |
+ SVID<-smapdata$SVIndex |
|
| 588 |
+ } |
|
| 589 |
+ else{
|
|
| 590 |
+ #smapdata <- readSMap_DLE(smap, input_fmt_smap) |
|
| 591 |
+ SVID<-smapdata$SmapEntryID |
|
| 592 |
+ } |
|
| 593 |
+ } |
|
| 594 |
+ else if(input_fmt_SV=="Text"){
|
|
| 595 |
+ if(EnzymeType == "SVMerge"){
|
|
| 596 |
+ smapdata <- readSMap(smappath, input_fmt_smap = "Text") |
|
| 597 |
+ SVID<-smapdata$SVIndex |
|
| 598 |
+ } |
|
| 599 |
+ else{
|
|
| 600 |
+ smapdata <- readSMap_DLE(smappath, input_fmt_smap = "Text") |
|
| 601 |
+ SVID<-smapdata$SmapEntryID |
|
| 602 |
+ } |
|
| 603 |
+ } |
|
| 604 |
+ else{
|
|
| 605 |
+ stop("Input format for SMAP Incorrect")
|
|
| 606 |
+ } |
|
| 607 |
+ ##Extracting Data |
|
| 608 |
+ overlapgenes <- stringr::str_trim(smapdata$OverlapGenes_strand_perc) |
|
| 609 |
+ |
|
| 610 |
+ |
|
| 611 |
+ dataOverLap <- data.frame(matrix(nrow = nrow(smapdata), ncol = 2)) |
|
| 612 |
+ ##Extracting Overlapped Genes |
|
| 613 |
+ #dataOverLap<-data.frame(matrix(nrow=10,ncol=5)) |
|
| 614 |
+ names(dataOverLap)<-c("SVID", "OverlapProbandTPM")
|
|
| 615 |
+ print("###OverlapGenes###")
|
|
| 616 |
+ for(kk in 1:length(overlapgenes)){
|
|
| 617 |
+ #print(paste("kk:",kk))
|
|
| 618 |
+ #for(kk in 1:10){
|
|
| 619 |
+ #print(kk) |
|
| 620 |
+ datOverLap<-data.frame() |
|
| 621 |
+ #print(paste("kk:",kk,sep=""))
|
|
| 622 |
+ svID<-as.character(SVID[kk]) |
|
| 623 |
+ if(length(grep(";",overlapgenes[kk]))>=1){
|
|
| 624 |
+ st1<-strsplit(as.character(overlapgenes[kk]), split = ";") |
|
| 625 |
+ sttemp<-as.character(st1[[1]]) |
|
| 626 |
+ #print("1")
|
|
| 627 |
+ gns_overlap<-c() |
|
| 628 |
+ for (tt in 1:length(sttemp)){
|
|
| 629 |
+ gn_temp<-strsplit(sttemp[tt], split = "\\(")
|
|
| 630 |
+ gns_overlap<-c(gns_overlap,as.character(gn_temp[[1]][1])) |
|
| 631 |
+ } |
|
| 632 |
+ |
|
| 633 |
+ datOverLap<-OverlapRNAseq_solo( |
|
| 634 |
+ gnsOverlap = as.character(gns_overlap), |
|
| 635 |
+ SVID = svID, |
|
| 636 |
+ RNASeqData = RNASeqData, |
|
| 637 |
+ pattern_Proband = pattern_Proband) |
|
| 638 |
+ |
|
| 639 |
+ } |
|
| 640 |
+ else if (length(grep("\\(", as.character(overlapgenes[kk]))) >= 1){
|
|
| 641 |
+ #print("2")
|
|
| 642 |
+ gnsOverlap<-strsplit(as.character(overlapgenes[kk]),split="\\(")[[1]][1]
|
|
| 643 |
+ datOverLap<-OverlapRNAseq_solo(gnsOverlap = as.character(gnsOverlap), |
|
| 644 |
+ SVID = svID, |
|
| 645 |
+ RNASeqData = RNASeqData, |
|
| 646 |
+ pattern_Proband = pattern_Proband) |
|
| 647 |
+ } |
|
| 648 |
+ else{
|
|
| 649 |
+ #print(paste("OverLapDNSVID:",svID))
|
|
| 650 |
+ datOverLap<-data.frame( |
|
| 651 |
+ SVID = svID, ProbandTPM = "-") |
|
| 652 |
+ } |
|
| 653 |
+ dataOverLap[kk,]<-c( |
|
| 654 |
+ as.character(datOverLap$SVID), |
|
| 655 |
+ Proband_OverlapGeneExpression_TPM = as.character(datOverLap$ProbandTPM)) |
|
| 656 |
+ } |
|
| 657 |
+ |
|
| 658 |
+ ##Extracting NonOverlapped Genes |
|
| 659 |
+ nearestUPGenes<-smapdata$Upstream_nonOverlapGenes_dist_kb |
|
| 660 |
+ #datanonOverLapUP<-data.frame(matrix(nrow=nrow(smapdata),ncol=5)) |
|
| 661 |
+ datanonOverLapUP<-data.frame(matrix(nrow = nrow(smapdata),ncol = 2)) |
|
| 662 |
+ names(datanonOverLapUP) <- c("SVID", "NonOverlapUPProbandTPM")
|
|
| 663 |
+ print("###NonOverlapUPStreamGenes###")
|
|
| 664 |
+ for(ll in 1:length(nearestUPGenes)) |
|
| 665 |
+ {
|
|
| 666 |
+ #for(ll in 1:10){
|
|
| 667 |
+ #print(ll) |
|
| 668 |
+ datNonOverLapUP <- data.frame() |
|
| 669 |
+ #print(paste("llUP:",ll,sep=""))
|
|
| 670 |
+ svID<-as.character(SVID[ll]) |
|
| 671 |
+ if(length(grep(";",nearestUPGenes[ll]))>=1){
|
|
| 672 |
+ st1<-strsplit( |
|
| 673 |
+ as.character(nearestUPGenes[ll]), |
|
| 674 |
+ split = ";") |
|
| 675 |
+ sttemp<-as.character(st1[[1]]) |
|
| 676 |
+ #print("1")
|
|
| 677 |
+ gns_nonoverlap_up<-c() |
|
| 678 |
+ for (mm in 1:length(sttemp)){
|
|
| 679 |
+ gn_temp<-strsplit(sttemp[mm],split="\\(")
|
|
| 680 |
+ gns_nonoverlap_up<-c(gns_nonoverlap_up, |
|
| 681 |
+ as.character(gn_temp[[1]][1])) |
|
| 682 |
+ } |
|
| 683 |
+ |
|
| 684 |
+ datNonOverLapUP<-nonOverlapRNAseq_solo( |
|
| 685 |
+ gnsNonOverlap = as.character(gns_nonoverlap_up), |
|
| 686 |
+ SVID = svID, |
|
| 687 |
+ RNASeqData = RNASeqData, |
|
| 688 |
+ pattern_Proband = pattern_Proband) |
|
| 689 |
+ |
|
| 690 |
+ } |
|
| 691 |
+ else if (length(grep( |
|
| 692 |
+ "\\(",as.character(nearestUPGenes[ll]))) >=1
|
|
| 693 |
+ ){
|
|
| 694 |
+ #print("2")
|
|
| 695 |
+ gnsNonOverlapUP<-strsplit(as.character(nearestUPGenes[ll]),split="\\(")[[1]][1]
|
|
| 696 |
+ |
|
| 697 |
+ datNonOverLapUP<-nonOverlapRNAseq_solo( |
|
| 698 |
+ gnsNonOverlap = as.character(gnsNonOverlapUP), |
|
| 699 |
+ SVID = svID,RNASeqData = RNASeqData, |
|
| 700 |
+ pattern_Proband=pattern_Proband) |
|
| 701 |
+ |
|
| 702 |
+ } |
|
| 703 |
+ else{
|
|
| 704 |
+ #print(paste("NonOverLapUPSVID:",svID))
|
|
| 705 |
+ datNonOverLapUP<-data.frame( |
|
| 706 |
+ SVID = svID, ProbandTPM="-" |
|
| 707 |
+ ) |
|
| 708 |
+ } |
|
| 709 |
+ datanonOverLapUP[ll,]<-c( |
|
| 710 |
+ as.character(datNonOverLapUP$SVID), |
|
| 711 |
+ Proband_Upstream_nonOverlapGeneExpression_TPM = as.character(datNonOverLapUP$ProbandTPM)) |
|
| 712 |
+ |
|
| 713 |
+ } |
|
| 714 |
+ |
|
| 715 |
+ ##Extracting NonOverlapped Down Stream Genes |
|
| 716 |
+ nearestDNGenes<-smapdata$Downstream_nonOverlapGenes_dist_kb |
|
| 717 |
+ datanonOverLapDN<-data.frame(matrix(nrow = nrow(smapdata), ncol = 2)) |
|
| 718 |
+ names(datanonOverLapDN)<-c("SVID","NonOverlapDNProbandTPM")
|
|
| 719 |
+ print("###NonOverlapDNStreamGenes###")
|
|
| 720 |
+ for(nn in 1:length(nearestDNGenes)) |
|
| 721 |
+ {
|
|
| 722 |
+ #for(nn in 1:10){
|
|
| 723 |
+ datNonOverLapDN<-data.frame() |
|
| 724 |
+ # print(paste("llDN:",ll,sep=""))
|
|
| 725 |
+ svID<-as.character(SVID[nn]) |
|
| 726 |
+ if(length(grep(";",nearestDNGenes[nn]))>=1){
|
|
| 727 |
+ st1 <- strsplit(as.character(nearestDNGenes[nn]), split = ";") |
|
| 728 |
+ sttemp<-as.character(st1[[1]]) |
|
| 729 |
+ #print("1")
|
|
| 730 |
+ gns_nonoverlap_dn<-c() |
|
| 731 |
+ for (mm in 1:length(sttemp)){
|
|
| 732 |
+ gn_temp <- strsplit(sttemp[mm],split="\\(")
|
|
| 733 |
+ gns_nonoverlap_dn <- c( |
|
| 734 |
+ gns_nonoverlap_dn,as.character(gn_temp[[1]][1]) |
|
| 735 |
+ ) |
|
| 736 |
+ } |
|
| 737 |
+ datNonOverLapDN<-nonOverlapRNAseq_solo( |
|
| 738 |
+ gnsNonOverlap = as.character(gns_nonoverlap_dn), |
|
| 739 |
+ SVID = svID,RNASeqData = RNASeqData, |
|
| 740 |
+ pattern_Proband = pattern_Proband) |
|
| 741 |
+ |
|
| 742 |
+ } |
|
| 743 |
+ else if (length(grep("\\(",as.character(nearestDNGenes[nn]))) >= 1){
|
|
| 744 |
+ # print("2")
|
|
| 745 |
+ gnsNonOverlapDN<-strsplit(as.character( |
|
| 746 |
+ nearestDNGenes[nn]),split="\\(")[[1]][1]
|
|
| 747 |
+ datNonOverLapDN<-nonOverlapRNAseq_solo( |
|
| 748 |
+ gnsNonOverlap = as.character(gnsNonOverlapDN), |
|
| 749 |
+ SVID = svID, |
|
| 750 |
+ RNASeqData = RNASeqData, |
|
| 751 |
+ pattern_Proband = pattern_Proband) |
|
| 752 |
+ |
|
| 753 |
+ } |
|
| 754 |
+ else{
|
|
| 755 |
+ #print(paste("NonOverLapDNSVID:",svID))
|
|
| 756 |
+ #print ("SVID")
|
|
| 757 |
+ datNonOverLapDN<-data.frame( |
|
| 758 |
+ SVID = svID,ProbandTPM="-") |
|
| 759 |
+ } |
|
| 760 |
+ datanonOverLapDN[nn,]<-c(as.character(datNonOverLapDN$SVID), |
|
| 761 |
+ Proband_Downstream_nonOverlapGeneExpression_TPM = as.character(datNonOverLapDN$ProbandTPM)) |
|
| 762 |
+ } |
|
| 763 |
+ |
|
| 764 |
+ dataFinal<-data.frame(smapdata, |
|
| 765 |
+ OverlapProbandEXP = dataOverLap[,2], |
|
| 766 |
+ NonOverlapUPprobandEXP = datanonOverLapUP[,2], |
|
| 767 |
+ NonOverlapDNprobandEXP = datanonOverLapDN[,2]) |
|
| 768 |
+ return(dataFinal) |
|
| 769 |
+ |
|
| 770 |
+} |
|
| 0 | 771 |
\ No newline at end of file |