[BioC] ChIPpeakAnno

[Julie Zhu]

Hi Som,

myPeakList is RangedData, where "start" is the start (or summit) of the
binding site, "end" is the end of the binding site, "names" is the name of
the binding site and "space" is the chromosome name.

Here is how to create RangedData myexp from a list of binding sites.

myexp = RangedData(IRanges(start = c(967654, 2010897, 2496704), end =
c(967754, 2010997, 2496804), names = c("Site1", "Site2", "Site3")), space =
c("1", "2", "3"))

Please see ?annotatePeakInBatch for more examples. Thanks!

Best regards,

Julie


*******************************************
Lihua Julie Zhu, Ph.D
Research Associate Professor
Program Gene Function and Expression
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 2/19/10 8:52 AM, "somnath bandyopadhyay" <genome1976 at hotmail.com> wrote:

> 
> Could anybody please tell me what the input list (myPeakList) for the
> ChIPpeakAnno program look like?
> 
> I have a list of probeset ids with genomic coordinates coming from a nimblegen
> 385k chip chip experiment.
> 
>  
> 
> Thanks in advance,
> 
> Som.
>  
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