On Mon, Jun 14, 2010 at 10:15 AM, pterry@huskers.unl.edu <
pterry@huskers.unl.edu> wrote:

>  Dear bioc-sig-sequencing,
>
> Regarding the "laneSubsample() in the chipseq package" suggestion.  Example
> usage for this from the chipseq manual shows
>
> laneSubsample(lane1, lane2, fudge = 0.05)
>
> with lane1 & lane2 parameters being of class "GenomeData".
>
> As noted, after reading in the two files (ctcf, gfp), I would have
> AignedRead objects.  I assume I would need to convert each to a GenomeData
> object to use the 'laneSubsample' command?
>
>
Yes. This would be as(ctcf, "GenomeData").


> I assume two GenomeData objects would be the output?  I would then need to
> convert the reduced size GenomeData object resulting from the initially
> larger GenomeData object, back to an AlignedRead object?  Then could proceed
> with the page 6 & 7 steps previously referenced to determine FDR cutoff.
>
>
No, I would not go back to AlignedRead. FDR cutoff can be determined using
GenomeData.

Just as a heads up, the chipseq package will probably be moving away from
these generic "GenomeData" containers. In this case, GRanges would be
appropriate, I think.


> Can someone indicate if this will work, and if so, indicate how to do it?
>  And if not, suggest how an FDR cutoff may be determined?
>
>
>
> Thanks,
> pterry@huskers.unl.edu
> P. Terry
>
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>
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