On 11/20/2011 07:45 PM, sutada Mungpakdee wrote:
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'])
Hi --
the quotations mismatch in the line above, leading to a syntax error.
IRanges is a Bioconductor package; you'll find a knowledgeable community
on the Bioconductor mailing list.
http://bioconductor.org/help/mailing-list/
Martin
#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
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
