R help - Feb 2012 - In R 2.14.1, what does wrong sign in 'by' argument mean?

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


which I never got before when running codes of this sort, infact I re ran
old code that worked perfectly before, except this time Im getting this
error message which doesn't seem to make any sense at all! I need help with
this before I go completely insane... Maybe Im just bad at this program, but
it seems to me that it has a mind of its own... I was also getting an error
message before regarding the ylim function, stating that it needed to be a
finite value, which is what I was giving it? HELP!!!

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> seq(1,4,1)
[1] 1 2 3 4
> seq(1,4,-1)
Error in seq.default(1, 4, -1) : wrong sign in 'by'
argument
>
On Tue, Feb 21, 2012 at 1:53 PM, bioinformatics <uccstudent@live.ie>
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
>
>
> which I never got before when running codes of this sort, infact I re ran
> old code that worked perfectly before, except this time Im getting this
> error message which doesn't seem to make any sense at all! I need help
with
> this before I go completely insane... Maybe Im just bad at this program,
> but
> it seems to me that it has a mind of its own... I was also getting an error
> message before regarding the ylim function, stating that it needed to be a
> finite value, which is what I was giving it? HELP!!!
>
> --
> View this message in context:
>
http://r.789695.n4.nabble.com/In-R-2-14-1-what-does-wrong-sign-in-by-argument-mean-tp4407926p4407926.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
>
http://www.R-project.org/posting-guide.html<http://www.r-project.org/posting-guide.html>
> and provide commented, minimal, self-contained, reproducible code.
>
	[[alternative HTML version deleted]]

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.