[BioC] ChiPpeakAnno: findOverlappingPeaks: running time

[Zhu, Lihua (Julie)]

George,

Thanks for the feedback! I noticed that you are using R 2.10.1 and an old
version of ChIPpeakAnno.

Could you please try to update to R 2.14 and ChIPpeakAnno 2.2 and see if
that help? Thanks!

Best regards,

Julie


On 1/16/12 1:53 PM, "George [guest]" <guest at bioconductor.org> 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!
> 
>  -- 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