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RNAseq_sexcheck.R

@@ -17,11 +17,9 @@ option_list <- list(
         help="The input expression files. required!"),
 	make_option(c("-e", "--type_gene_id"),type="character", default="EnsemblID",
         help="The type of gene symbol. Could be either of EnsemblID/EntrezID/GeneSymbol [default: EnsemblID]"),
-	make_option(c("-b", "--pre_lowexpr_filtered"), metavar="FALSE",default=FALSE,
-        help="Where pre-filterd low expressed genes. [default: FALSE]"),
     make_option(c("-s", "--sex_genes"),type="character",  default="./sexgenelist.txt",
         help="File in tab-delimited format sex gene list with EnsemblID/EntrezID/GeneSymbol. [default: ./sexgenelist.txt ]"),
-   make_option(c("-p", "--project_code"), type="character",default="rnaseq",
+    make_option(c("-p", "--project_code"), type="character",default="rnaseq",
         help="Project code, which is used as prefix of output file. [default: rnaseq]")
 		)
 		
@@ -29,6 +27,8 @@ option_list <- list(
 # otherwise if options not found on command line then set defaults, 
 opt <- parse_args(OptionParser(option_list=option_list))
 
+message("NOTE: If low expresssed genes were filtered, this analysis might be successful. ")
+
 #pre analysis
 if (is.null(opt$input)){
   print_help(opt_parser)
@@ -50,42 +50,49 @@ sexgene<-read.delim(opt$sex_genes,header=T,stringsAsFactors=F,check.names=F)
 
 #
 if(grepl("Ensembl",opt$type_gene_id,ignore.case=T)){
-sexgenelist<-as.character(sexgene$EnsemblID)
+message("The type of gene symbol is set: EnsembleID. Could be either of EnsemblID/EntrezID/GeneSymbol.")
+malegene<-as.character(sexgene$EnsemblID[grep("^M",sexgene$SexSpecific,ignore.case=T)])
+femalegene<-as.character(sexgene$EnsemblID[grep("^F",sexgene$SexSpecific,ignore.case=T)])
 }
+
 if(grepl("Entrez",opt$type_gene_id,ignore.case=T)){
-sexgenelist<-as.character(sexgene$EntrezID)
+message("The type of gene symbol is set: EntrezID. Could be either of EnsemblID/EntrezID/GeneSymbol.")
+malegene<-as.character(sexgene$EntrezID[grep("^M",sexgene$SexSpecific,ignore.case=T)])
+femalegene<-as.character(sexgene$EntrezID[grep("^F",sexgene$SexSpecific,ignore.case=T)])
 }
+
 if(grepl("Symbol",opt$type_gene_id,ignore.case=T)){
-sexgenelist<-as.character(sexgene$GeneSymbol)
+message("The type of gene symbol is set: GeneSymbol. Could be either of EnsemblID/EntrezID/GeneSymbol.")
+malegene<-as.character(sexgene$GeneSymbol[grep("^M",sexgene$SexSpecific,ignore.case=T)])
+femalegene<-as.character(sexgene$GeneSymbol[grep("^F",sexgene$SexSpecific,ignore.case=T)])
 }
 
-sexexpr<-logexpr[rownames(logexpr) %in% sexgenelist, ]
 
-if(nrow(sexexpr)<=(length(sexgenelist)/2)){
-  stop("Not sufficent expression profile sex specific genes were detected for sex prediction. Please check rowname is matched with type_gene_id in the command.", call.=FALSE)
-}
+male_expr<-logexpr[rownames(logexpr) %in% malegene, ]
+female_expr<-logexpr[rownames(logexpr) %in% femalegene, ]
 
-#get median value without 
-#if pre_lowexpr_filtered = FALSE, remove not expressed values before obtaining median value 
+if(nrow(male_expr)<(length(malegene))){
+  stop("Not sufficent expression profile male-specific genes were detected for sex prediction. Please check rowname is matched with type_gene_id in the command.", call.=FALSE)
+}
 
-if (opt$pre_lowexpr_filtered){
-medians<-apply(logexpr,2,median)
-}else{
-minvalue<- min(as.numeric(logexpr)[!is.na(as.numeric(logexpr))])
-medians<-apply(logexpr,2,function(x){median(x[which(x> minvalue)])})
+if(nrow(female_expr)<(length(female_expr))){
+  stop("Not sufficent expression profile female-specific genes were detected for sex prediction. Please check rowname is matched with type_gene_id in the command.", call.=FALSE)
+}
+s<-c()
+male_expr_t<-t(male_expr)
+female_expr_t<-t(female_expr)
+for (i in 1:nrow(female_expr)){
+s<-cbind(s,male_expr_t-female_expr_t[,i])
 }
 
-#sexexpr1<-sexexpr[apply(sexexpr,1,function(x){length(which(x<( -6)))}<13),]
+sexpredict<-data.frame(
+SampleID=colnames(logexpr),
+Sex=apply(s,1,function(x){ifelse(length(which(x<0))>=8,"Female","Male")}))
+
+rownames(sexpredict)<-c(1:nrow(sexpredict))
 
-#if all of the genes expressed lower than median: female, else male
-sexpredict<-ifelse(rowSums(apply(sexexpr,1,function(x){ifelse(x-medians>0,1,0)}))>2,"Male","Female")
-sexpredict_tab<-data.frame(
-Sample=names(sexpredict),
-Sex=sexpredict
-)
-rownames(sexpredict_tab)<-c(1:nrow(sexpredict_tab))
+write.csv(sexpredict,paste(out_dir,opt$project_code,"_sexpredict.csv",sep=""),quote=F,row.names=F)
+saveRDS(sexpredict,paste(out_dir,opt$project_code,"_sexpredict.rds",sep=""))
 
-write.csv(sexpredict_tab,paste(out_dir,opt$project_code,"_sexpredict.csv",sep=""),quote=F,row.names=F)
-saveRDS(sexpredict_tab,paste(out_dir,opt$project_code,"_sexpredict.rds",sep=""))
 message("RNAseq_sexcheck.R finished!")