[BioC] ChiPpeakAnno: findOverlappingPeaks: running time

[Martin Morgan]

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
>>
>
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>
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