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
