Thanks so much for clarifying this behavior and how this subseq() operation
will work when you use x[1] instead of x[[1]].  I was at a loss for why it
was behaving this way until you pointed this out!

Andrew

On Wed, May 26, 2010 at 2:35 PM, Steve Lianoglou <
mailinglist.honeypot@gmail.com> wrote:

> Woops, small type in my example:
>
> ## assigning `<-` into a DNAString in *this* context will fail
> R> subseq(x[1], 2, 3) <- NULL
> Error in `[[<-`(`*tmp*`, 1, value = <S4 object of class "DNAString">) :
>  no method for assigning subsets of this S4 class
>
> Should have been:
> R> subseq(x[[1]], 2, 3) <- NULL
>
> Not sure how that slipped through like that, sorry.
>
> Btw:
>
> sessionInfo()
> R version 2.11.0 Patched (2010-05-05 r51909)
> x86_64-apple-darwin9.8.0
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices datasets  utils     methods   base
>
> other attached packages:
> [1] Biostrings_2.16.0 IRanges_1.7.1
>
> loaded via a namespace (and not attached):
> [1] Biobase_2.8.0
>
> --
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
>  | Memorial Sloan-Kettering Cancer Center
>  | Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact
>

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