R version 3.2.3 (2015-12-10) -- "Wooden Christmas-Tree"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R是自由软件，不带任何担保。
在某些条件下你可以将其自由散布。
用'license()'或'licence()'来看散布的详细条件。

R是个合作计划，有许多人为之做出了贡献.
用'contributors()'来看合作者的详细情况
用'citation()'会告诉你如何在出版物中正确地引用R或R程序包。

用'demo()'来看一些示范程序，用'help()'来阅读在线帮助文件，或
用'help.start()'通过HTML浏览器来看帮助文件。
用'q()'退出R.

> 
> ss <- function(TP,TN,FP,FN,bet=1){
+ 	if (is.na(TP)) TP=0
+ 	if (is.na(TN)) TN=0
+ 	if (is.na(FP)) FP=0
+ 	if (is.na(FN)) FN=0
+ 	sen=TP/(TP+FN)
+ 	spe=TN/(TN+FP)
+ 	pre=TP/(TP+FP)
+ 	f = (1+bet^2)*pre*sen/(bet^2*pre+sen)
+ 	return(c(sen,spe,pre,f))
+ }
> 
> log_up <- function(x){
+ 	ids = which(x<=0)
+ 	x[ids] = 0.0000001
+ 	return(log10(x))
+ }
> library(ggplot2)
> 
> args = (commandArgs(trailingOnly = T))
> print (args)
[1] "finput=\"giremi_out\""   "fout=\"giremi_out.res\""
> for (i in 1:length(args)){
+ 	eval(parse(text=args[[i]]))
+ }
> 
> #dat <- read.table(file=finput,header=F,row.names=1,comment.char="")
> dat <- read.table(file=finput,header=T,comment.char="")
> rownames(dat) = paste(dat[,"chr"],dat[,"coor"],dat[,"strand"],sep="|")
> dat = cbind(dat,0)
> colnames(dat) <- c("chr","coordinate","strand","ifSNP","gene","reference_base","upstream_1base","downstream_1base","major_base","major_count","tot_count","major_ratio","if_MI","MI","pvalue_MI","estimated_allelic_ratio","ifNEG","if_GLM","pvalue_GLM","RNAE_t","A","C","G","T","ifRNAE")
> ids = which(dat[,"major_base"]=="N")
> if (length(ids)>0) dat = dat[-ids,] 
> dat[rownames(subset(dat,pvalue_MI>0 & pvalue_MI<=0.05 & ifSNP==0)),"ifRNAE"]= 1
> dat.pos <- subset(dat, pvalue_MI>0 & pvalue_MI <= 0.01 & ifSNP==0 & RNAE_t == "AG")
> if (nrow(dat.pos)==0){
+ dat.pos <- subset(dat, pvalue_MI>0 & pvalue_MI <= 0.05 & ifSNP==0 & RNAE_t == "AG")
+ }
> dat.neg <- subset(dat,ifNEG == 1)
> #dat.neg <- subset(dat,ifNEG == 1 & RNAE_t=="AG")
> dat.unknown = subset(dat,ifRNAE==0 & ifSNP ==0 & RNAE_t=="AG")
> 
> dat.pos <- cbind(dat.pos[,c("upstream_1base","downstream_1base")],abs(dat.pos[,"major_ratio"]-dat.pos[,"estimated_allelic_ratio"]),1)
Error in data.frame(..., check.names = FALSE) : 
  参数值意味着不同的行数: 0, 1
Calls: cbind -> cbind -> data.frame
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