[Bioc-sig-seq] weird interaction between BSgenome (getSeq) and ChIPpeakAnno

Janet Young jayoung at fhcrc.org
Thu Feb 24 01:06:35 CET 2011

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.

Error in x[[name, exact = FALSE]] : 
  missing '[[' method for Sequence class GRanges

thanks (yet again),



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



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)

> 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':


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)

 [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            

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      

More information about the Bioc-sig-sequencing mailing list