[BioC] Hypergeometric test in ChIPpeakAnno

[Zhu, Lihua (Julie)]

Abihishek,

This is a very good question which has been very nicely addressed by Noah.
Please follow the following email threads in the Biocondutor mailing
archives.
https://stat.ethz.ch/pipermail/bioconductor/2010-November/036540.html
http://permalink.gmane.org/gmane.science.biology.informatics.conductor/29476
http://permalink.gmane.org/gmane.science.biology.informatics.conductor/30115

Please cc bioconductor <bioconductor at stat.math.ethz.ch> so that others could
benefit and/or contribute. Thanks!

Best regards,

Julie


On 6/28/11 4:29 AM, "Abhishek Singh" <abhisheksinghnl at gmail.com> wrote:

> Dear prof. Julie,
> 
> I have one more question regarding the hypergeometric test implemented in
> ChIPpeakAnno package for construction of Venn diagram.
> 
> The command you gave for the sample data in the article is:
> 
>> makeVennDiagram(RangedDataList(Peaks.Ste12.Replicate1,
>> Peaks.Ste12.Replicate2, Peaks.Ste12.Replicate3), NameOfPeaks =
>> c("Replicate1","Replicate2","Replicate3"), maxgap = 0, totalTest = 1580)
> 
> Where totalTest indicates how many peaks in total that is used in
> hypergeometric test (as indicated in article).
> 
> Imagine I have a three data sets:
> (a) Dataset A has 100 peaks
> (b) Dataset B has 150 peaks
> (c) Dataset C has 75 peaks
> 
> How can I compute the value of totalTest for these three data sets?
> 
> Thank you for  your time,
> Looking forward for your reply,
> 
> Regards
> Abhishek
> 
> 
> On Mon, Jun 27, 2011 at 7:45 PM, Abhishek Singh <abhisheksinghnl at gmail.com>
> wrote:
>> Dear Prof. Julie,
>> 
>> Thank you, for providing code.
>> 
>> Best Regards,
>> Abhishek
>> 
>> 
>> On Mon, Jun 27, 2011 at 5:47 PM, Zhu, Lihua (Julie) <Julie.Zhu at umassmed.edu>
>> wrote:
>>> Abhishek,
>>> 
>>> Please try the following code snippets assuming your bed file is test1.bed
>>> without header.
>>> 
>>> library(ChIPpeakAnno)
>>> test1.bed=read.table("~/Document/test1.bed", sep="\t", skip=0, header=FALSE)
>>> myPeakList = BED2RangedData(test1.bed,header=FALSE)
>>>   
>>> 
>>> Now you can use annotatePeakInBatch to annotate myPeakList.
>>> 
>>> For detailed information on how to use ChIPpeakAnno package, please refer to
>>> http://www.bioconductor.org/packages/2.8/bioc/vignettes/ChIPpeakAnno/inst/do
>>> c/ChIPpeakAnno.pdf,
>>>  http://www.bioconductor.org/help/course-materials/2010/BioC2010/BioC2010_Ch
>>> IPpeakAnno.pdf
>>> And Zhu L.J. et al. (2010) ChIPpeakAnno: a Bioconductor package to annotate
>>> ChIP-seq and ChIP-chip data. BMC Bioinformatics 2010,
>>> 11:237doi:10.1186/1471-2105-11-237.
>>> 
>>> 
>>> Best regards,
>>> 
>>> Julie 
>>> 
>>> 
>>> On 6/27/11 7:40 AM, "Abhishek Singh" <abhisheksinghnl at gmail.com
>>> <http://abhisheksinghnl@gmail.com> > wrote:
>>> 
>>>> hi!
>>>> 
>>>> I was trying to use your R package ChIPpeakAnno to annotate my peak files
>>>> which are in .bed format.
>>>> 
>>>> Somehow I am unable to tell your package to load my input files and perform
>>>> analysis. 
>>>> 
>>>> To brief you what exactly I intend to do, I have a peak file (form MACS in
>>>> .bed format) and I want to give this file as an input to your package in R
>>>> (which is already installed).
>>>> 
>>>> could you roughly tell me what exactly should I do so that the package
>>>> starts reading my files as an input.
>>>> 
>>>> Thank you for your time.
>>>> 
>>>> Looking forward for your reply.
>>>> 
>>>> Regards
>>>> Abhishek A. Singh
>>>> 
>> 
> 
>