[Bioc-devel] getSeq Development Version Error

[Dario Strbenac]

Hello,

Is this an unimplemented feature or a bug somewhere ?

> x
GRanges with 2 ranges and 0 elementMetadata values
    seqnames           ranges strand |
       <Rle>        <IRanges>  <Rle> |
[1]     chr1 [ 99900, 100099]      + |
[2]     chr2 [199900, 200099]      + |

seqlengths
      chr1      chr2
 247249719 242951149

> BSgenome::getSeq(Hsapiens, x, as.character=FALSE)
Error in .extractSeqsFromDNAString(subject, ranges(grg), strand(grg)) : 
  could not find function "unsplit.list.of.XStringSet"

> sessionInfo()
R version 2.14.0 Under development (unstable) (2011-06-08 r56096)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8    
 [5] LC_MONETARY=en_AU.UTF-8    LC_MESSAGES=en_AU.UTF-8   
 [7] LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BSgenome.Hsapiens.UCSC.hg18_1.3.17 BSgenome_1.21.0                   
[3] Biostrings_2.21.5                  GenomicRanges_1.5.11              
[5] zoo_1.6-5                          IRanges_1.11.8                    
[7] Repitools_0.99.0                  

--------------------------------------
Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010
Australia