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

[Janet Young]

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/

------------------------------------------------------------------- 




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> 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