Dear Ramu, It is a RangedData. Please take a look at the 2nd example given in the Bioc2010 meeting in Seattle. http://www.bioconductor.org/help/course- materials/2010/BioC2010/BioC2010_ChI PpeakAnno.pdf You can also get more information in a R session with the following functions. library(ChIPpeakAnno) ?annotatePeakInBatch browseVignettes("ChIPpeakAnno") Kind regards, Julie ******************************************* Lihua Julie Zhu, Ph.D Research Associate Professor Program in Gene Function and Expression Program in Molecular Medicine University of Massachusetts Medical School 364 Plantation Street, Room 613 Worcester, MA 01605 508-856-5256 http://www.umassmed.edu/pgfe/faculty/zhu.cfm On 8/12/10 6:22 AM, "Ramu Chenna" <ramu.chenna at="" biotec.tu-="" dresden.de=""> wrote: > Hello Julie Zhu, > > A quick question regarding your chipseq paper in BMC bioinformatics > (2010). > Could you just show me the sample of mypeaklist (should it be in bed > format or...) > > Thanks > Ramu

Dear Ramu, Glad it worked. Thanks for letting me know! Kind regards, Julie On 8/16/10 5:44 AM, "Ramu Chenna" <ramu.chenna at="" biotec.tu-="" dresden.de=""> wrote: > Dear Julie > > It works, thanks. Basically what we wanted to do is, from the peak > list, we want to know > how many peaks are in promotor regions and further classify them into > cpg island promotors and > non-cpg island promoters. > > Note: The pdf documentation is not done correct there are lines that are > truncated, (may be a problem in setting the margin in latex?) > > Best, > Ramu > > Zhu, Julie wrote: >> Dear Ramu, >> >> You can use read.table to read the data in bed file format from MACS, then >> use BED2RangedData to convert the data to RangedData. >> >> Library(ChIPpeakAnno) >> X = read.table("mypeak.bed",sep="\t") >> MyPeakList = BED2RangeData(X) >> >> ?BED2RangedData >> >> BTW, I am on vacation so may not be able to check email frequently. >> >> Kind regards, >> >> Julie >> >> >> On 8/13/10 3:44 AM, "Ramu Chenna" <ramu.chenna at="" biotec.tu-="" dresden.de=""> wrote: >> >> >>> Dear Julie, >>> >>> The link did not work, but I found the ppt. Thanks. >>> >>> I am not a R geek, and I just need to know how to read MACS output >>> as say 'myPeakList' as RangedData. It would be nice to know there is already >>> a R function doing this. >>> >>> Regards, >>> Ramu >>> >>> Zhu, Julie wrote: >>> >>>> Dear Ramu, >>>> >>>> It is a RangedData. Please take a look at the 2nd example given in the >>>> Bioc2010 meeting in Seattle. >>>> http://www.bioconductor.org/help/course- materials/2010/BioC2010/BioC2010_Ch>>>> I >>>> PpeakAnno.pdf >>>> >>>> >>>> >>>> >>>> >>>> >> >> >> >

Dear Ramu, I would suggest download the CpG island track from UCSC and make a RangedData, then annotate your binding sites with the CpG island. Kind regards, Julie On 8/17/10 4:00 AM, "Ramu Chenna" <ramu.chenna at="" biotec.tu-="" dresden.de=""> wrote: > Dear Julie, > > Is there way way to classify binding sites into classify promotors > into cpg-island and non-cpg islands? > > Best > Ramu > > Zhu, Julie wrote: >> Dear Ramu, >> >> Glad it worked. Thanks for letting me know! >> >> Kind regards, >> >> Julie >> >> >> On 8/16/10 5:44 AM, "Ramu Chenna" <ramu.chenna at="" biotec.tu-="" dresden.de=""> wrote: >> >> >>> Dear Julie >>> >>> It works, thanks. Basically what we wanted to do is, from the peak >>> list, we want to know >>> how many peaks are in promotor regions and further classify them into >>> cpg island promotors and >>> non-cpg island promoters. >>> >>> Note: The pdf documentation is not done correct there are lines that are >>> truncated, (may be a problem in setting the margin in latex?) >>> >>> Best, >>> Ramu >>> >>> Zhu, Julie wrote: >>> >>> >