删除 'RNAseq_1_ballgown.R'

RNAseq_1_ballgown.R

@@ -1,73 +0,0 @@
-#!/usr/bin/env Rscript
-# example:
-# Rscript RNAseq_1_ballgown.R -o /home/yuying/rnaseqreport_test -i ./ballgown/ -l FALSE -p test 
-# Rscript RNAseq_1_ballgown.R -o /home/yuying/rnaseqreport_test -i ./ballgown/ 
-
-
-suppressPackageStartupMessages(library("optparse"))
-suppressPackageStartupMessages(library("ballgown"))
-
-# specify our desired options in a list
-# by default OptionParser will add an help option equivalent to 
-# make_option(c("-h", "--help"), action="store_true", default=FALSE, 
-#               help="Show this help message and exit")
-
-option_list <- list( 
-    make_option(c("-o", "--out_dir"), type="character",default="./",
-        help="The output directory [default ./]"),
-    make_option(c("-i", "--input"),type="character", default=NULL,
-        help="The directory input of expression files. It is output from ballgown software."),
-    make_option(c("-f", "--floor_value"),metavar="number",default=0.01,
-        help="A number to add to each value before log2 transformation to avoid infinite value.[default: 0.01]"),
-    make_option(c("-l", "--log2_norm"), metavar="TRUE", default=TRUE,
-        help="Perform log2 transformation on FPKM value. [default: TRUE]"),
-	make_option(c("-p", "--project_code"), type="character",default="rnaseq",
-        help="Project code, which is used as prefix of output file. [default: rnaseq]")
-		)
-
-# get command line options, if help option encountered print help and exit,
-# otherwise if options not found on command line then set defaults, 
-opt <- parse_args(OptionParser(option_list=option_list))
-
-if (is.null(opt$input)){
-  print_help(opt_parser)
-  stop("At least one argument must be supplied (input file).", call.=FALSE)
-}
-
-#generate FPKM expression profile from ballgown outputs
-geballgown_expr <- ballgown(dataDir =  opt$input ,samplePattern = ".*",meas = "all")
-expr <- gexpr(geballgown_expr)     
- message("finish ballgown\n")
-
-#remove _1P and FPKM from colnames, _1P is from alicloud app, FPKM is added due to default output of stringtie/ballgown. 
-nam<-colnames(expr)
-nam<-gsub("_1P$","",nam)
-nam<-gsub("^FPKM.","",nam)
-colnames(expr) <- nam
-
-out_dir<-paste(gsub("/$","",opt$out_dir),"/",sep="")
-
-if(opt$log2_norm==TRUE){
-message("start log2 transformation\n")
-
-logexpr<-apply(expr,2,function(x){log2(x+as.numeric(opt$floor_value))})
-logexpr_out<-cbind(rownames(logexpr),round(logexpr,3))
-colnames(logexpr_out)[1]<-"Gene"
-
-message("output log2 expression file\n")
-
-write.table(logexpr_out,file = paste(out_dir,opt$project_code,"_geneexp_log2fpkm_floor0p01_c",ncol(logexpr),"r",nrow(logexpr),"_",Sys.Date(),".txt",sep=""),sep="\t",row.names=F,quote=F)
-}else{ 
-
-#output expression file with fpkm 
-expr<-cbind(rownames(expr),round(expr,3))
-colnames(expr)[1]<-"Gene"
-
-message("output fpkm expression file\n")
-
-write.table(expr,file = paste(out_dir,opt$project_code,"_geneexp_fpkm_c",ncol(expr),"r",nrow(expr),"_",Sys.Date(),".txt",sep=""),sep="\t",row.names=F,quote=F)
-}
-
-
-
-