Dingxia,

You can use addGeneIDs to add other IDs. Please type ?addGeneIDs in R to see examples.

Regarding your question to get sequence, you can pass mart object into the function to do that or forge your own BSgenome data package. Here is the link on how to forge your own BSgenome data package http://www.bioconductor.org/packages/2.10/bioc/vignettes/BSgenome/inst/doc/BSgenomeForge.pdf. If you have questions regarding this, please email the list and the developer. For passing mart object to fetch sequences,  please type ?getAllPeakSequence in R to see the documentation. Alternatively, you could also use biomart package.

Could you please keep the thread in the list so that others can contribute and/or benefit? Thanks!

Best regards,

Julie



On 8/29/12 10:23 PM, "Dingxia Feng" <fengdxia@iastate.edu> wrote:

Hello, julie,

Thanks for the help. I can see the histogram and pie chart now.

I'll ask you a favor to modify the code a liitle, so I can see the gene public names. Now I  can see the Gene WB IDs, but I'd like to have gene public names, because they are more friendly. For example, if I see lin-10 (gene public name), then immediately I know what's this gene for, however, I'll have no idea if I see WBGene00002999 (gene WB ID).

Thanks.

Best regards.

On 8/29/12 10:43 PM, "Dingxia Feng" <fengdxia@iastate.edu> wrote:

Hi, Julie,


I tried "available.genomes(splitNameParts=FALSE, type=getOption("pkgType"))" , then I found for c.elegans, the available genomes are  "BSgenome.Celegans.UCSC.ce2"  and
"BSgenome.Celegans.UCSC.ce6", not the one I want (ws220=ce10). Does this mean I can't use ChIPpeakAnno to fetch sequences for motif discovery? Thanks.


Best.

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