Hello Janet. First, we are not tired of your posts. For instance, your catch of the bug in the reduce() function will save hours of frustration for many users. Thank you.
Second, the getSeq() problem that you find after loading ChIPpeakAnno seems to be solved in the devel branch (see sessionInfo below). I tested it following your steps but with BSgenome.Mmusculus.UCSC.mm9. Not that it actually matters but I chose this genome because it has 3 million Ns at the beginning of every chromosome (except chrY). I hope this helps. Ivan ######################################################## > sessionInfo() R version 2.13.0 Under development (unstable) (2010-12-02 r53747) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 [5] LC_MONETARY=C LC_MESSAGES=en_US.utf8 [7] LC_PAPER=en_US.utf8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] ChIPpeakAnno_1.7.0 limma_3.7.23 [3] org.Hs.eg.db_2.4.6 GO.db_2.4.5 [5] RSQLite_0.9-4 DBI_0.2-5 [7] AnnotationDbi_1.13.13 BSgenome.Ecoli.NCBI.20080805_1.3.17 [9] multtest_2.7.1 Biobase_2.11.8 [11] biomaRt_2.7.1 BSgenome.Mmusculus.UCSC.mm9_1.3.17 [13] BSgenome_1.19.3 Biostrings_2.19.9 [15] GenomicRanges_1.3.18 IRanges_1.9.22 loaded via a namespace (and not attached): [1] MASS_7.3-11 RCurl_1.5-0 splines_2.13.0 survival_2.36-5 [5] XML_3.2-0 Ivan Gregoretti, PhD National Institute of Diabetes and Digestive and Kidney Diseases National Institutes of Health 5 Memorial Dr, Building 5, Room 205. Bethesda, MD 20892. USA. Phone: 1-301-496-1016 and 1-301-496-1592 Fax: 1-301-496-9878 On Wed, Feb 23, 2011 at 7:06 PM, Janet Young <[email protected]> wrote: > Hi again, > > (sorry, you're probably tired of hearing from me now). > > I have just started to play with ChIPpeakAnno - it looks like it might be > very useful for me. However, once I load it I get an error from BSgenome's > getSeq function. Here's the error alone (myregions_RD is a RangedData > object), and below is my full code. > > getSeq(Cfamiliaris,myregions_RD) > Error in x[[name, exact = FALSE]] : > missing '[[' method for Sequence class GRanges > > > thanks (yet again), > > Janet > > ------------------------------------------------------------------- > > Dr. Janet Young (Trask lab) > > Fred Hutchinson Cancer Research Center > 1100 Fairview Avenue N., C3-168, > P.O. Box 19024, Seattle, WA 98109-1024, USA. > > tel: (206) 667 1471 fax: (206) 667 6524 > email: jayoung ...at... fhcrc.org > > http://www.fhcrc.org/labs/trask/ > > ------------------------------------------------------------------- > > > > > R version 2.12.1 (2010-12-16) > Copyright (C) 2010 The R Foundation for Statistical Computing > ISBN 3-900051-07-0 > Platform: x86_64-unknown-linux-gnu (64-bit) > > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain conditions. > Type 'license()' or 'licence()' for distribution details. > > Natural language support but running in an English locale > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > >> library(IRanges) > > > Attaching package: 'IRanges' > > The following object(s) are masked from 'package:base': > > cbind, eval, Map, mapply, order, paste, pmax, pmax.int, pmin, > pmin.int, rbind, rep.int, table > > > >> library(BSgenome.Cfamiliaris.UCSC.canFam2) > Loading required package: BSgenome > Loading required package: GenomicRanges > Loading required package: Biostrings > >> myregions_RD <- >> RangedData(IRanges(start=c(100001L,2000001L),end=c(100100L,2000100L)),space=c("chr1","chr2"),strand=c("+","+") >> ) > >> getSeq(Cfamiliaris,myregions_RD) > [1] > "NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN" > [2] > "NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN" > >> library(ChIPpeakAnno) > Loading required package: biomaRt > Loading required package: multtest > Loading required package: Biobase > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > > > Attaching package: 'Biobase' > > The following object(s) are masked from 'package:IRanges': > > updateObject > > Loading required package: BSgenome.Ecoli.NCBI.20080805 > Loading required package: GO.db > Loading required package: AnnotationDbi > Loading required package: DBI > Loading required package: org.Hs.eg.db > Loading required package: limma > >> getSeq(Cfamiliaris,myregions_RD) > Error in x[[name, exact = FALSE]] : > missing '[[' method for Sequence class GRanges > >> sessionInfo() > R version 2.12.1 (2010-12-16) > Platform: x86_64-unknown-linux-gnu (64-bit) > > 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_1.6.0 > [2] limma_3.6.9 > [3] org.Hs.eg.db_2.4.6 > [4] GO.db_2.4.5 > [5] RSQLite_0.9-4 > [6] DBI_0.2-5 > [7] AnnotationDbi_1.12.0 > [8] BSgenome.Ecoli.NCBI.20080805_1.3.16 > [9] multtest_2.7.1 > [10] Biobase_2.10.0 > [11] biomaRt_2.6.0 > [12] BSgenome.Cfamiliaris.UCSC.canFam2_1.3.16 > [13] BSgenome_1.18.3 > [14] Biostrings_2.18.2 > [15] GenomicRanges_1.2.3 > [16] IRanges_1.8.9 > > loaded via a namespace (and not attached): > [1] MASS_7.3-11 RCurl_1.5-0 splines_2.12.1 survival_2.36-5 > [5] XML_3.2-0 > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
