[BioC] Minimal input data format for bsseq

[Kasper Daniel Hansen]

This is all you need.  Look at the bsseq constructor.

Kasper

On Fri, Dec 21, 2012 at 6:40 PM, Aryee, Martin,Ph.D.
<Aryee.Martin at mgh.harvard.edu> wrote:
> Hi Kasper,
>
> I'd like to use bsseq on a partially preprocessed whole genome bisulfite sequencing dataset. I have a data table with one row per CpG and columns for:
>
> 1. chromosome
> 2. position
> 3. number of reads supporting an unmethylated CpG (U)
> 3. number of reads supporting a methylated CpG (M)
>
> Is it possible to turn this into an acceptable input for bsseq (perhaps with reduced functionality), or is it essential to run the BSmooth alignment suite to generate the complete set of columns typically used by bsseq?
>
> Thanks,
> Martin
>
>
>
>
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