On Mon, Jun 14, 2010 at 10:15 AM, [email protected] < [email protected]> 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, > [email protected] > P. Terry > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
