[BioC] Error in getting exons sequence

[Valerie Obenchain]

Hello,

This code works for me in both release and devel.

library(GenomicFeatures)
library(BSgenome.Hsapiens.UCSC.hg19)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)

txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
tx_Exons <- exonsBy(txdb)
tx1<-tx_Exons[1:3]
seq<-getSeq(Hsapiens,tx1)
>> seq
> DNAStringSetList of length 3
> [["1"]] CTTGCCGTCAGCCTTTTCTTTGACCTCTTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCCAGACT...
> [["2"]] CTTGCCGTCAGCCTTTTCTTTGACCTCTTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCCAGACT...
> [["3"]] CTTGCCGTCAGCCTTTTCTTTGACCTCTTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCCAGACT...


What is your sessionInfo()? I've included my below.

Valerie



 > sessionInfo()
R version 3.1.0 Patched (2014-04-18 r65405)
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=en_US.UTF-8    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] parallel  stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
  [1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0
  [2] BSgenome.Hsapiens.UCSC.hg19_1.3.99
  [3] BSgenome_1.32.0
  [4] Biostrings_2.32.0
  [5] XVector_0.4.0
  [6] GenomicFeatures_1.16.2
  [7] AnnotationDbi_1.26.0
  [8] Biobase_2.24.0
  [9] GenomicRanges_1.16.3
[10] GenomeInfoDb_1.0.2
[11] IRanges_1.22.9
[12] BiocGenerics_0.10.0

loaded via a namespace (and not attached):
  [1] BatchJobs_1.2           BBmisc_1.6              BiocParallel_0.6.1 

  [4] biomaRt_2.20.0          bitops_1.0-6            brew_1.0-6 

  [7] codetools_0.2-8         DBI_0.2-7               digest_0.6.4 

[10] fail_1.2                foreach_1.4.2           GenomicAlignments_1.0.1
[13] iterators_1.0.7         plyr_1.8.1              Rcpp_0.11.2
[16] RCurl_1.95-4.1          Rsamtools_1.16.0        RSQLite_0.11.4
[19] rtracklayer_1.24.2      sendmailR_1.1-2         stats4_3.1.0
[22] stringr_0.6.2           tools_3.1.0             XML_3.98-1.1
[25] zlibbioc_1.10.0


On 07/30/2014 08:06 AM, Asma rabe wrote:
> Hi,
>
> When I tried to get the exons sequence, I got an error..
>
>
> library("BSgenome.Hsapiens.UCSC.hg19")
>
> txdb<-TxDb.Hsapiens.UCSC.hg19.knownGene
>
>
> tx_Exons<-exonsBy(txdb)
>
>   tx1<-tx_Exons[1:3]
>
>
> (seq<-getSeq(Hsapiens,tx1))
>
> Error in .toGRanges(names, strand) : invalid 'names'
>
> Any help is apreciated
> Thank you.
>
> 	[[alternative HTML version deleted]]
>
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-- 
Valerie Obenchain
Program in Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, Seattle, WA 98109

Email: vobencha at fhcrc.org
Phone: (206) 667-3158