[R] coverage plot

[sutada Mungpakdee]

Hi,

I'm very beginner for R but I think it is a time to start as it is very useful.

I have a coverage read file (illusmp454merCbed) for whole genome ~ 450 Mbp. This is head of this file.
Scaffold	sca_position	coverage
Scaffold1	1	0
Scaffold1	2	0
Scaffold1	3	0
Scaffold1	4	0
Scaffold1	5	0
Scaffold1	6	0
Scaffold1	7	1
Scaffold1	8	3
Scaffold1	9	3

I would like to plot everage coverage for every 1 kbp for whole genome. May I use R as below? Should I use IRanges?

data <-read.table(file="~/q20snpref/illusmp454merCbed",sep="\t",header=F)
colnames(data)<-c("Scaffold","sca_position","coverage")
depth<-mean(data[,"coverage'])
#depth now has the mean (overall)coverage
#set the bin-size
window<-1001 
rangefrom<-0
rangeto<-length(data[,"sca_position"])
data.1kb<-runmean(data[,"coverage"],k=window)
png(file="cov_1k.png",width=400,height=1000)
plot(x=data[rangefrom:rangeto,"sca_position"],y=data.1kb[rangefrom:rangeto],pch=".",cex1,xlab="bp position",ylab="depth",type="p")
dev.off()

I got these error.
  
Error: unexpected symbol in:
"rangefrom<-0
rangeto<-length(data[,"sca_position"
> data.1kb<-runmed(data[,"coverage"],k=window)
Error in as.integer(k) : 
  cannot coerce type 'closure' to vector of type 'integer'
> png(file="cov_1k.png",width=400,height=1000)
> plot(x=data[rangefrom:rangeto,"sca_position"],y=data.1kb[rangefrom:rangeto],pch=".",cex1,xlab="bp position",ylab="depth",type="p")
Error in `[.data.frame`(data, rangefrom:rangeto, "sca_position") : 
  object 'rangefrom' not found

I thought that I have done thing wrong, any suggestion will be very helpful.

Best regards,
Sutada