Hi Khademul, Thank you very much for the great suggestions! I have implemented BED2RangedData as well as GFF2RangedData in ChIPpeakAnno_1.2.2 for converting BED/GFF format to RangedData before calling annotatePeakInBatch. Please let me know if you encounter any problems. Thanks! Best regards, Julie > > > On 11/27/09 12:12 PM, "Khademul Islam" <khademul.islam@gmail.com> wrote: > >> Hello Dr. Julie, >> >> >> It would be really really helpful, specially who has only little knowledge >> about R, if you impliment "bed2RangedData" function. It will be pretty >> straight forward use of the bed file that is generated by peak calling >> softwares. >> >> If you already have version with this function, I would be happy to >> try.............. >> >> Thanks again >> >> Khademul >> > > ******************************************* > Lihua Julie Zhu, Ph.D > Research Associate Professor > Program 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 > > >> [[alternative HTML version deleted]]

Julie Zhu wrote: > Hi Khademul, > > Thank you very much for the great suggestions! > > I have implemented BED2RangedData as well as GFF2RangedData in > ChIPpeakAnno_1.2.2 for converting BED/GFF format to RangedData before > calling annotatePeakInBatch. Please let me know if you encounter any > problems. Thanks! better to use rtracklayer::import -- no need to duplicate existing functions. Martin > Best regards, > > Julie >> >> On 11/27/09 12:12 PM, "Khademul Islam" <khademul.islam at="" gmail.com=""> wrote: >> >>> Hello Dr. Julie, >>> >>> >>> It would be really really helpful, specially who has only little knowledge >>> about R, if you impliment "bed2RangedData" function. It will be pretty >>> straight forward use of the bed file that is generated by peak calling >>> softwares. >>> >>> If you already have version with this function, I would be happy to >>> try.............. >>> >>> Thanks again >>> >>> Khademul >>> >> ******************************************* >> Lihua Julie Zhu, Ph.D >> Research Associate Professor >> Program 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 >> >> > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793