[R] coverage plot

[Martin Morgan]

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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