ChiPpeakAnno: findOverlappingPeaks: running time
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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.
GO ChIPpeakAnno GO ChIPpeakAnno • 551 views
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@martin-morgan-1513
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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 -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
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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 >
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Julie Zhu ★ 4.3k
@julie-zhu-3596
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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
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