Hello,

if you omit calling the detail function, the result will be an
AlignedGenomeIntervals object:

library1_sense <- library1[strand(library1)=="+"]

while the result of the "detail" function is a data.frame.

And if the object containing the genes is of class
"Genome_intervals_stranded" the strand will be taken into account, if it is
of class "Genome_intervals" without strand information, the strand does not
matter. Hope this answers your question.

Best regards,
Joern

On Thu, Apr 28, 2011 at 2:44 AM, <karlerhard@berkeley.edu> wrote:

>
> Hello all,
>
> I've been using the girafe package to make counts tables for two nascent
> transcript libraries (overlap between aligned reads and genes), which I am
> comparing directly.  I would like to check if there's a difference between
> "sense" and "antisense" tags within genic regions.
>
> I thought I could do this easily by making the following object:
>
> library1_sense <- detail(library1[strand(library1)=="+"])
>
> and then using it in the interval_overlap with the list of annotated
> genes.  However, the resulting object is a data frame and not an
> AlignedGenomeIntervals object, which interval_overlap seems to need.
>
> Is there some way around this?  Maybe a way to force strandedness in the
> interval_overlap function?  Or another way to create a subset of "+" or
> "-" strand reads while maintaining the AlignedGenomeIntervals format?
> I've been reading the manual but I can't find a way to do this.
>
> thanks for any help you can offer!
>
>
> Karl Erhard
> Graduate Student
> UC Berkeley
>

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