Hi Kelly,

let us assume that the package name of your successfully created custom
BSgenome for e.g. 'oryza sativa' is 'BSgenome.OryzaSativa' and that it is
installed in your R environment using R CMD INSTALL <package>.

First load your custom BSgenome object into your R session using
library(BSgenome.OryzaSativa)

Note, BSgenome.OryzaSativa will not appear in the list returned by
available.genomes(). However, in case the library is loaded you should be
able to immediately use it as usual in MEDIPS like

library(MEDIPS)
BSgenome=    "BSgenome.OryzaSativa"
MSet = MEDIPS.createSet(file="oryza.bam", BSgenome=BSgenome)

Lukas




On Wed, Dec 18, 2013 at 6:57 AM, Vining, Kelly <Kelly.Vining@oregonstate.edu
> wrote:

>
> ________________________________
> From: Vining, Kelly
> Sent: Tuesday, December 17, 2013 10:58 AM
> To: 'Lukas Chavez'
> Cc: bioconductor@r-project.org
> Subject: RE: [BioC] Question about MEDIPS extend parameter
>
> Hello BioC group,
> have created a BSgenome object for my genome of interest, and it is in my
> current working directory. I now want to use it with MEDIPS. How do I make
> it appear under
> >available.genomes()? Is it necessary for my custom genome to appear in
> this list for me to be able to use it with MEDIPS? Or is there a different
> method for accessing this object?
>
> Thanks much,
> --Kelly V.
>
>
>
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