make_tiles_for_TES

####This function is for making tiles for the TES regions###########

make_tiles_for_TES<-function(x){

        gff0_genome_location<-read.table("/Users/dongliguo/Documents/reference_sequences/A_nidulans/annotation/A_nidulan_10_gene_final_annotation2.bed")
        x1<-read.table(x)
        asd_in_gene_name<-as.character(x1$V1)

        gene_location_name<-as.character(gff0_genome_location$V4)
        gff0_genome_location2<-as.matrix(gff0_genome_location)
        chr_region<-matrix(0,ncol=5,nrow=length(asd_in_gene_name))
                for ( i in 1:length(asd_in_gene_name) )
                {
                        chr_region[i,]<-gff0_genome_location2[asd_in_gene_name[i]==as.character(gff0_genome_location$V4),]
                }
        write.table(chr_region,file="inter_file.bed",sep="\t",quote=FALSE,row.names=FALSE,col.names=FALSE)
        gene_select_region_CreA<-import.bed("inter_file.bed")
        A_value<-NULL
                for( i in 1:length(end(ranges(gene_select_region_CreA))))
                {
                        A_value[i]=0
                }
        tiles2=sapply(1:length(end(ranges(gene_select_region_CreA))),function(i)
                if(gene_select_region_CreA$score[i]=="1")
                        A_value[i]+seq(end(ranges(gene_select_region_CreA))[i]-500,end(ranges(gene_select_region_CreA))[i]+1500,length.out=321)
                else
                        A_value[i]+seq(end(ranges(gene_select_region_CreA))[i]+500,end(ranges(gene_select_region_CreA))[i]-1500,length.out=321))
                        Chromatin_length<-read.table("/Users/dongliguo/Documents/reference_sequences/A_nidulans/annotation/genome.size")
        si<-Seqinfo(seqnames=as.character(Chromatin_length$V1),seqlengths=Chromatin_length$V2,genome="A_nidulans")
        tiles_3 = GRanges(tilename = paste( rep(gene_select_region_CreA$name, each=321), 1:321, sep="_" ),
                        seqnames = Rle( rep(as.character(seqnames(gene_select_region_CreA)),each=321)),
                        ranges=IRanges(start=as.vector(tiles2),
                        width=50),
                        strand=Rle(rep("*",length(as.vector(tiles2)))),
                        seqinfo=si)
        return(tiles_3)
        }
        
############################