[BioC] ChIPpeakAnno Paper - Example Dataset not found

[Zhu, Julie]

Dear Dietmar,

Thank you very much for the feedback of the paper and the package!

Where did you download the package and what is the package version? It could
be that the dataset was not included in the old version.

I would recommend you to download the package 1.4.1 using the following code
in R 2.11.

source("http://bioconductor.org/biocLite.R")
biocLite("ChIPpeakAnno")

I just downloaded the package and the dataset is in the data folder. Please
let me know if you encounter any problems.

Regarding your 2nd question, only the nearest gene will be reported.

I am ccing Bioconductor mailing list so that others can benefit if
encountering the same problem. Thanks for trying the package and for the
precise and concise feedback!

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 6/25/10 7:27 AM, "DIETMAR FERNANDEZ ORTH" <dfernandez045 at ikasle.ehu.es>
wrote:

> Dear Dr. Zhu,
> 
> I have just read the paper you and your colleagues have written
> "ChIPPeakAnno: a Bioconductor package to..." (PMID=20459804) and I
> found it very interesting I have just begun to analyze ChipSeq data
> and I found your tool very useful. Anyway, I have some problems maybe
> you could explain me.
> 
> 1)
> On page 3 you wrote " For fast access, transcription star sites from
> common genomes such as... TSS.human.GRCh37.... were included as
> prebuilt annotation data packages". The problem is that when following
> your first example:
> 
> data (TSS.human.GRCh37)
> 
> I get the following error:
> 
> In data(TSS.human.GRCh37) : data set 'TSS.human.GRCh37' not found
> 
> In fact, when looking in the zip file "RData" in Program
> Files\R\R-2.10.0\library\ChIPpeakAnno\data, the file TSS.human.GRCh37
> isn't there.
> 
> Am I doing something wrong?
> 
> Is it maybe that the file isn't attach? Where could I download the file?
> 
> 
> 2)
> When you get the genes near to your peaks, in case there was one gene
> in a distance of 20pb for my peak and another one in a distance of 40
> pb, is it possible to get the informatión about this 2 genes or would
> I get information only about the first one?
> 
> 
> Thanks in advance
> 
> Dietmar
> 
> 
>