[BioC] assignChromosomeRegion in 2.6.0 ChIPpeakAnno

[Stefan Pinter]

Hi Julie, 

well, I was more thinking of something along the lines of either:

a.) Over/Under-representation:
Percentage of exons in genome = 2%
Percentage of peaks overlapping exons = 10%
Exons are 5-fold over-represented

But I realize now, that will only work with a full annotation, not a custom annotation.

b.) something like the jaccard index used in bedtools:

total length of intersection / total length of union

http://en.wikipedia.org/wiki/Jaccard_index

Just suggestions, there are probably many more possible ways to calculate a score.
Thank you,
- Stefan.

----- Original Message -----
From: "Lihua Zhu (Julie)" <Julie.Zhu at umassmed.edu>
To: "Stefan Pinter" <pinter at molbio.mgh.harvard.edu>
Cc: "<bioconductor at r-project.org>" <bioconductor at r-project.org>
Sent: Friday, March 15, 2013 1:28:09 PM
Subject: Re: [BioC] assignChromosomeRegion in 2.6.0 ChIPpeakAnno

Stefan,

Regarding the enrichment/depletion score, Does the following toy example
illustrate how to calculate such score? If not, could you please give a toy
example? Thanks!

For example, if the total number of peaks = 100, number of peaks assigned to
promoter = 90, number of peaks assigned to enhancer = 10, then the
enrichment score = 90% and 10% for promoter region and enhancer region
respectively.

We will add closest to annotatePeakInBatch in the dev version. Thanks for
the great suggestion!

Please cc bioconductor at r-project.org. Thanks!

Best regards,

Julie


On 3/15/13 12:26 PM, "Stefan Pinter" <pinter at molbio.mgh.harvard.edu> wrote:

> Sure, thank you Julie.
> 
> Yes, that is what I meant. Since all the necessary information (peak
> locations, feature locations, total count, total length) are already available
> in RangedData & Annotation, it would be very convenient to calculate
> enrichment/depletion and possibly even significance scores (by permutation) on
> the fly. The significance score may be overkill, but if the function at least
> reported enrichment/depletion scores, the user could always supply a number of
> shuffled ranges to build a random model of enrichment scores and calculate
> significance after.
> 
> In addition, would it be possible to add another definition for
> PeakLocForDistance in annotatePeakInBatch?
> PeakLocForDistance = "start means using start of the peak to calculate the
> distance to feature"
> 
> It would be helpful to have "closest", meaning distance to feature measured
> from peak start or peak end, whichever is closer. That would help with broad
> peaks, which using "middle" for isn't very helpful.
> 
> Thank you and Best wishes,
> - Stefan.
> 
> ----- Original Message -----
> From: "Lihua Zhu (Julie)" <Julie.Zhu at umassmed.edu>
> To: "Stefan Pinter" <pinter at molbio.mgh.harvard.edu>
> Cc: "<bioconductor at r-project.org>" <bioconductor at r-project.org>
> Sent: Friday, March 15, 2013 8:06:03 AM
> Subject: Re: [BioC] assignChromosomeRegion in 2.6.0 ChIPpeakAnno
> 
> Stefan,
> 
> You can download 2.6.1 to directly use assignChromosomeRegion without the
> package prefix (I updated last night and it might take sometime to propagate
> to the installation site). To find out what parameters supported by the
> function, in R, please type help( ChIPpeakAnno:::assignChromosomeRegion).
> You will see that indeed PeakLocForDistance is not supported. If needed, I
> can add such parameter.
> 
> Also regarding your previous suggestion of adding enrichment status of
> feature length, do you mean enrichment of peaks in certain category of
> chromosome region? For example, a significant enrichment score with 90%
> peaks in promoter region would be interesting.
> 
> Could you please keep the thread in the Bioc for others to
> contribute/benefit? Thanks!
> 
> Best regards,
> 
> Julie
> 
> 
> On 3/14/13 10:10 PM, "Stefan Pinter" <pinter at molbio.mgh.harvard.edu> wrote:
> 
>> PPS. I think PeakLocForDistance is not working in that function:
>> 
>>> l.feat.dRF8.100k <-ChIPpeakAnno:::assignChromosomeRegion(rda.dRF8, TSS,
>>> Exon,
>>> utr5, utr3, proximal.promoter.cutoff=100000,
>>> immediate.downstream.cutoff=100000, PeakLocForDistance="middle")
>> Error in ChIPpeakAnno:::assignChromosomeRegion(rda.dRF8, TSS, Exon, utr5,  :
>>   unused argument(s) (PeakLocForDistance = "middle")
>>> l.feat.dRF8.100k <-ChIPpeakAnno:::assignChromosomeRegion(rda.dRF8, TSS,
>>> Exon,
>>> utr5, utr3, proximal.promoter.cutoff=100000,
>>> immediate.downstream.cutoff=100000, PeakLocForDistance= middle)
>> Error in ChIPpeakAnno:::assignChromosomeRegion(rda.dRF8, TSS, Exon, utr5,  :
>>   unused argument(s) (PeakLocForDistance = middle)
>>> l.feat.dRF8.100k <-ChIPpeakAnno:::assignChromosomeRegion(rda.dRF8, TSS,
>>> Exon,
>>> utr5, utr3, proximal.promoter.cutoff=100000,
>>> immediate.downstream.cutoff=100000, PeakLocForDistance = c("middle"))
>> Error in ChIPpeakAnno:::assignChromosomeRegion(rda.dRF8, TSS, Exon, utr5,  :
>>   unused argument(s) (PeakLocForDistance = c("middle"))
>> 
>> ----- Original Message -----
>> From: "Stefan Pinter" <pinter at molbio.mgh.harvard.edu>
>> To: "Lihua Zhu (Julie)" <Julie.Zhu at umassmed.edu>
>> Sent: Thursday, March 14, 2013 9:39:10 PM
>> Subject: Re: [BioC] assignChromosomeRegion in 2.6.0 ChIPpeakAnno
>> 
>> PS. if I might add a simple feature addition to that function - it would be a
>> TRUE/FALSE trigger for whether to also report enrichment/depletion stats
>> based
>> on feature lengths, i.e. 50% peaks labeled as intergenic (or enhancers) is
>> less interesting than 50% of peaks reported as exonic (much greater
>> enrichment
>> as total exonic feature length is smaller). Thanks, Best...S
>> 
>> ----- Original Message -----
>> From: "Stefan Pinter" <pinter at molbio.mgh.harvard.edu>
>> To: "Lihua Zhu (Julie)" <Julie.Zhu at umassmed.edu>
>> Cc: "bioconductor" <bioconductor at r-project.org>
>> Sent: Thursday, March 14, 2013 9:32:33 PM
>> Subject: Re: [BioC] assignChromosomeRegion in 2.6.0 ChIPpeakAnno
>> 
>> Hi Julie,
>> 
>> yes, that worked! Thank you for the quick help, I very much appreciate it!
>> Thank you and Best wishes,
>> - Stefan.
>> 
>> ----- Original Message -----
>> From: "Lihua Zhu (Julie)" <Julie.Zhu at umassmed.edu>
>> To: "Lihua Zhu (Julie)" <Julie.Zhu at umassmed.edu>, "Stefan Pinter"
>> <pinter at molbio.mgh.harvard.edu>
>> Cc: "<bioconductor at r-project.org>" <bioconductor at r-project.org>
>> Sent: Thursday, March 14, 2013 8:50:51 PM
>> Subject: Re: [BioC] assignChromosomeRegion in 2.6.0 ChIPpeakAnno
>> 
>> Stefan,
>> 
>> Thanks for reporting this! Actually the function assignChromosomeRegion  is
>> not exported.
>> 
>> Could you please try the following to see if you can use it? Thanks!
>> 
>> ChIPpeakAnno:::assignChromosomeRegion
>> 
>> Best regards,
>> 
>> Julie
>> 
>> 
>> On 3/14/13 7:36 PM, "Lihua Julie Zhu" <julie.zhu at umassmed.edu> wrote:
>> 
>>> Stefan,
>>> 
>>> Could you please send me the sessionInfo? I just want to make sure you
>>> installed version 2.6.0. Thanks!
>>> 
>>> I noticed that when I try to install ChIPpeakAnno with the following code, I
>>> get 2.4 version instead.
>>> 
>>> source("http://bioconductor.org/biocLite.R")
>>> biocLite("ChIPpeakAnno")
>>> 
>>> Best regards,
>>> 
>>> Julie