#pre-process the cufflinks outputfile and cast the read_group into readscount matrix
#This script was written by Qi Zhao from Ren's Lab in SYSU.
#If you have any questions or suggestions, please contact the author by emali: zhaoqi3@mail2.sysu.edu.cn for details
library(reshape2)
getcufflinksReadsCounts<-function(cufflinksfile){
#read cufflinks read_group file
data<-read.table(cufflinksfile,header=T,sep="\t")
#reduce the data valume
data<-data[,1:4]
#asign varibles
attach(data)
#specify sample names
sample_name<-paste(condition,replicate,sep="_")
#new dataset for dcast
data2<-data.frame(tracking_id,sample_name,raw_frags)
#clean environment
rm(data)
#dcast dataset
result<-dcast(data2, tracking_id ~ sample_name, value.var='raw_frags')
detach(data)
row.names(result)<-result[,1]
result<-round(result[,-1])
return(result)
}
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