[Bioc-sig-seq] subsetting a ShortReadQ object

[Martin Morgan]

On 04/12/2010 07:15 PM, joseph wrote:
> Hello
> I have a ShortReadQ object (rfq) and a ShortRead object (rf) where sread(rf) is a subset of sread(rfq)
> How can I filter the ShortReadQ object (rfq) based on sread(rf)? 
> 

Hi Joseph --

if id(rfq) and id(rf) are both present (and BStringSets) then you could

  rfq[unlist(vwhichPDict(id(rf), id(rfq)))]

if the id's are not present you could try the same approach with the
sread()'s, but there's no guarantee that they would be unique.

Hope that helps,

Martin

> rfq[sread(rf)]
> Error in .nextMethod(x = x, i = i, ...) : invalid subscript type
>  thanks for the help
> Joseph
> 
> 
> 
>       
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

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