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Guest User ★ 12k@guest-user-4897
Last seen 7.1 years ago
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:  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C  LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8  LC_MONETARY=C LC_MESSAGES=en_US.UTF-8  LC_PAPER=en_US.UTF-8 LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C  LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  ChIPpeakAnno_1.2.15 limma_3.2.3  org.Hs.eg.db_2.3.6 GO.db_2.3.5  RSQLite_0.9-4 DBI_0.2-5  AnnotationDbi_1.8.2 BSgenome.Ecoli.NCBI.20080805_1.3.16  BSgenome_1.14.2 Biostrings_2.14.12  IRanges_1.4.16 multtest_2.2.0  Biobase_2.6.1 biomaRt_2.2.0 loaded via a namespace (and not attached):  MASS_7.3-4 RCurl_1.6-10 splines_2.10.1 survival_2.35-7  tools_2.10.1 XML_3.4-2 > -- Sent via the guest posting facility at bioconductor.org.