[BioC] ChiPpeakAnno: findOverlappingPeaks: running time

[Zhu, Lihua (Julie)]

Martin,

Thanks for the response! Indeed, ChIPpeakAnno levarges IRanges::findOverlaps
for finding overlaps among peaks.

Best regards,

Julie


On 1/16/12 2:06 PM, "Martin Morgan" <mtmorgan at fhcrc.org> wrote:

> On 01/16/2012 10:53 AM, George [guest] wrote:
>> 
>> I am attempting to perform an overlap of 85,000 TFS peaks with 73,000 Dnase1
>> hypersensitivity sites.  The tool took probably 45 minutes.  As CisGenome is
>> able to perform these overlaps very quickly, I am wondering if this time
>> frame seems correct?  I also noticed that the annotation is taking much
>> longer than CisGenome...
>> thanks, the ChiPpeakAnno software package looks very cool so far!
> 
> Not a regular ChIPeakAnno user, but some of the operations can be
> readily implemented using GRanges:: or IRanges:: findOverlaps and
> friends, and these will be very fast for the size of data you mention.
> 
> Martin
> 
>> 
>>   -- output of sessionInfo():
>> 
>>> sessionInfo()
>> R version 2.10.1 (2009-12-14)
>> x86_64-unknown-linux-gnu
>> 
>> locale:
>>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>   [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>>   [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>> 
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>> 
>> other attached packages:
>>   [1] ChIPpeakAnno_1.2.15                 limma_3.2.3
>>   [3] org.Hs.eg.db_2.3.6                  GO.db_2.3.5
>>   [5] RSQLite_0.9-4                       DBI_0.2-5
>>   [7] AnnotationDbi_1.8.2                 BSgenome.Ecoli.NCBI.20080805_1.3.16
>>   [9] BSgenome_1.14.2                     Biostrings_2.14.12
>> [11] IRanges_1.4.16                      multtest_2.2.0
>> [13] Biobase_2.6.1                       biomaRt_2.2.0
>> 
>> loaded via a namespace (and not attached):
>> [1] MASS_7.3-4      RCurl_1.6-10    splines_2.10.1  survival_2.35-7
>> [5] tools_2.10.1    XML_3.4-2
>>> 
>> 
>> --
>> Sent via the guest posting facility at bioconductor.org.
>> 
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>