I think this has been fixed in devel already. See: https://stat.ethz.ch/pipermail/bioconductor/2010-October/035985.html
Thanks, Michael On Wed, Feb 23, 2011 at 4:06 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 > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
