trait <- c("e:/QT_10s.qassoc.adjusted") gff <- c("browser position chr5:1-1000000\n") gff <- paste(gff,'browser hide all\n',sep="") gff <- paste(gff,'browser pack refGene encodeRegions\n',sep="") gff <- paste(gff,'browser full altGraph\n',sep="") gff <- paste(gff,'track type=wiggle_0 name="',trait,'" description="26/6/08" visibility=full maxHeightPixels=30 autoScale=off viewLimits=0:8 color=0,100,200 yLineMark=7 yLineOnOff=off',sep="") write.table(gff,file=paste(d1,trait,".gff",sep=""),row.names=FALSE,col.names=FALSE,dec=".",quote=FALSE,append=FALSE) restab <- read.fwf(file=trait,widths=c(4,12,rep(11,8)),skip=1) restab <- restab[,1:4] names(restab) <- c("CHR","SNP","UNADJ","GC") restab[,"SNP"]<-gsub(" ","",as.character(restab[,"SNP"])) restab[,1] <- paste("chr",restab[,1],sep="") restab <- merge(restab,SNP, by.x="SNP", by.y="Name", all.x = FALSE, all.y = FALSE) restab[,"Position2"] <- restab[,"Position"]+1 restab[,"GC"] <- format.pval(-log10(restab[,"GC"]),digits=1) restab$Chromosome <- as.numeric(as.character(restab$Chromosome)) restab<-restab[order(restab$Chromosome,restab$Position),] write.table(restab[,c("CHR","Position","Position2","GC")],file=paste(trait,".gff",sep=""),sep="\t",row.names=FALSE,col.names=FALSE,dec=".",quote=FALSE,,append=TRUE)