[Bioc-sig-seq] Reducing Solexa's export.txt in preparation for aChIP-seq analysis.

[Deepayan Sarkar]

On 3/19/09, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> Hi Ivan --

[...]

>  chipseq is in the devel branch, and data structures there have not
>  been fully aligned with other established structures, and vice versa,
>  and the chipseq data structures are not fully described.  This is a
>  disconnect that we're working to resolve before the release.
>
>  Others might have something else to say.

You'll find these scripts more current:

http://www.bioconductor.org/workshops/2009/SeattleJan09/ChIP-seq/

The use of "AlignedList" has been superceded by the "GenomeData" and
"GenomeDataList" classes defined in the BSgenome package. You can
convert an "AlignedRead" object to a "GenomeData" object by

as(obj, "GenomeData")

(which basically strips off everything except alignment location). To
work with a list of "GenomeData" objects (e.g. different lanes), see
?GenomeDataList.

-Deepayan