[BioC] narrow and xstringset

[Valerie Obenchain]

Hi,

On 08/11/14 06:20, carol white wrote:
> Hi,
> How can narrow be used with a dnastring? because when i use it with an instance of dnastring I get
>
> Error in (function (classes, fdef, mtable)Â  :
>   unable to find an inherited method for function ‘narrow’ for signature ‘"DNAString"’

That's correct. There is no narrow() method for DNAString.

>
>
> and when i convert the instance of dnastring with
>
> DNAStringSet(toString(str))
>
>
> and use with narrow with any value for end and width
>
>
> I get
>
> Error in .Call2("solve_user_SEW", refwidths, start, end, width, translate.negative.coord,  :
> Â  solving row 1: 'allow.nonnarrowing' is FALSE and the supplied end (500) is > refwidth + 1
>
>

In your other email on the list (title 'iranges') I explained how 
'start' and 'end' work for narrow(). My guess is that was the problem here.


d <- DNAString("TTGAAAA-CTC-N")

Conversion to string is not necessary, the DNAStringSet can be created 
with the DNAString.
 > DNAStringSet(d)
   A DNAStringSet instance of length 1
     width seq
[1]    13 TTGAAAA-CTC-N


Specify 'start' to begin 3 positions in (greater than) from the current 
start.
 > narrow(DNAStringSet(d), 3)
   A DNAStringSet instance of length 1
     width seq
[1]    11 GAAAA-CTC-N


Valerie

>
> Look forward to your reply,
>
> carol
>
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>
>
>
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-- 
Valerie Obenchain
Program in Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, Seattle, WA 98109

Email: vobencha at fhcrc.org
Phone: (206) 667-3158