[Bioc-sig-seq] Like subseq() but with the ability to accept a vector of starts

[Ivan Gregoretti]

Hi Michael and Martin,

Views() works great, specially for large chromosomes.

Problem solved.

Thank you,

Ivan



On Wed, Jun 1, 2011 at 12:25 PM, Michael Lawrence
<lawrence.michael at gene.com> wrote:
>
>
> On Wed, Jun 1, 2011 at 9:06 AM, Ivan Gregoretti <ivangreg at gmail.com> wrote:
>>
>> Hello IRanges connoisseurs,
>>
>> Is there a function like subseq() but with the ability to accept a
>> vector of starts?
>>
>>
>> For instance, if I want to chop the beginning of the murine
>> mitochondrial DNA into 50 nucleotides, I'd do
>>
>> library(BSgenome.Mmusculus.UCSC.mm9)
>>
>> subseq(Mmusculus[["chrM"]], start=1,   width=50)
>> subseq(Mmusculus[["chrM"]], start=51,  width=50)
>> subseq(Mmusculus[["chrM"]], start=101, width=50)
>> ...
>>
>> however, it would be more convenient something like this
>>
>> subseq(Mmusculus[["chrM"]], start=c(1,51,101), width=50)
>>
>
> So you would expect a DNAStringSet back? That is a little strange:
> subsetting a DNAString into a DNAStringSet. Perhaps you really want some way
> to "split" the DNAString into pieces.
>
> In this case, I would suggest using Views. You can use breakIntoChunks in
> order to form the ranges component.
>
> Michael
>
>> Thank you
>>
>> Ivan
>>
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>
>