On Tue, Feb 21, 2012 at 10:53:44AM -0800, bioinformatics wrote:
> Here is my code
>
>
> slidingwindowplotATGC = function(windowsize, inputseq)
> {
>
> starts = seq(1, length(inputseq)-windowsize, by = windowsize)
> n = length(starts)
> chunkGs = numeric(n)
> chunkAs = numeric(n)
> chunkTs = numeric(n)
> chunkCs = numeric(n)
> for (i in 1:n) {
> chunk = windowsize[starts[i]:(starts[i]+9999)]
> chunkG = sum("g" == chunk)/length(chunk)
> chunkA = sum("a" == chunk)/length(chunk)
> chunkT = sum("t" == chunk)/length(chunk)
> chunkC = sum("c" == chunk)/length(chunk)
> chunkGs[i] = chunkG
> chunkAs[i] = chunkA
> chunkTs[i] = chunkT
> chunkCs[i] = chunkC
> }
>
> plot(starts,chunkGs,type="b",ylim=c(min(min(chunkAs),min(chunkTs),min(chunkCs),min(chunkGs)),max(max(chunkAs),max(chunkTs),max(chunkCs),max(chunkGs))),col
> = "red")
> points(starts,chunkTs,col = "blue")
> points(starts,chunkAs,col = "green")
> points(starts,chunkCs)
> }
>
>
> Im getting the following error message,
>
> Error in seq.default(1, length(inputseq) - windowsize, by = windowsize)
> :
> wrong sign in 'by' argument
>
Hi.
Try to set options(error=utils::recover) before the run. When
the error occurs, you can see the values of the variables
inside the function, where the error occured.
Hope this helps.
Petr Savicky.
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