[Bioc-sig-seq] determining start position for QualityAlignedXStringSet output from pairwiseAlignment()

[Patrick Aboyoun]

Andrew,

start(subject(myalign))

should get you what you are looking for.

Cheers,
Patrick


On 4/28/10 5:07 PM, Andrew Yee wrote:
> I'm using pairwiseAlignment() in the Biostrings package as follows:
>
>
> library('Biostrings')
>
> pattern<- DNAString('GCGAGAG')
> subject<- DNAString('AGCTTTAGAGGCGAGAGGCAT')
>
> myalign<- pairwiseAlignment(pattern, subject)
> subject(myalign)
>
>    
>> subject(myalign)
>>      
> [11] GCGAGAG
>
> I'm interested in the position where the pattern starts aligning with the
> subject.  In this case, subject(myalign) gives 11 as the starting position
> as part of the print out.  Is there a way to pull out this starting position
> information from subject(myalign)?
>
> Thanks,
> Andrew
>
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